Digimon World 2 Walkthrough
Digimon World 2 is a very grindy dungeon crawler, you're going to be spending a lot of time doing the same things and exploring the same places over and over. Many of the dungeons in this game look the same and throughout the story you'll end up exploring the same dungeon multiple times for different objectives. Another thing that divides people on this game is how slow combat is as a whole.
Every move you make during battle will have its own animation and splash screen. Basically, every time a Digimon does anything it will show the name of the move and the Digimon along with the casting animation for that attack. This whole process takes 5 - 10 seconds per Digimon per attack. For this reason the main advice people give online is to use an Emulator when you play this game and to use the Fast Forward/Turbo Speed options in the Emulator. I personally played with my game sped up 500%, but I would recommend at minimum 250%.
250% speed is fast enough that you don't feel like you're wasting time but also not so fast that it messes up normal gameplay. Another thing many people recommend is to use a code that gives Unlimited/Infinite Bits. This game was designed in such a way to make you grind for hours to get anywhere and these two things decrease the amount of 'tedious' grind significantly. If you'd like to see a list of available codes check out my Digimon World 2 Codebreaker Codes.
Of course, it's ultimately your decision how you play--I am just making recommendations on ways to make the experience better. I personally feel these changes did improve the experience for me, so they may for you too. With all of that out of the way, let's dive in!
When you first start this game you're going to be given a long introduction sequence that teaches you about the story and the dungeons that you will be exploring. These dungeons are the main gameplay loop of the game. Like it shows you at the start, you will talk with an NPC then choose a dungeon to explore and you will traverse it with your Digi-Beetle. Inside each dungeon you'll find a variety of traps and Digimon to fight.
Your primary goal in these dungeons is to reach the last floor (the walls will look different on the final floor) and defeat the boss. This will complete the dungeon and advance the story; occasionally you will have different goals in a dungeon other than beating the boss. We'll talk about these when they happen.
After completing the game's introduction you will gain access to the whole city unrestricted (pictured above). Your task now is to join one of three different teams, I strongly encourage you to choose the Gold Hawks which specialize in Vaccine type Digimon.
The whole internet seems to agree that the Gold Hawks have the easiest time during the early game because of the available Digimon. Basically, you can only capture the Digimon available to your guild early in the game. There are other restrictions too, but this is the main one. As a Gold Hawk you can also get Metal Greymon on the fourth mission if you pick up a Toy Plane prior, I will talk more about this later.
Below are the Digimon that are available to each of the guilds:
Gold Hawks: Vaccine Digimon
Blue Falcons: Data Digimon
Black Sword: Virus Digimon
For this guide, I recommend you choose Gold Hawks. My first time playing through the game I chose the Gold Hawks and it was still very tedious with all of the leveling I had to do, but from what I read it could of been worse. This time I will be choosing Blue Falcons who use Data Digimon because this is what most people agree to be the worst choice.
Keep in mind, you can choose whatever you want! All it means is more (or less) grinding for you in the early game. Either way, it's still going to be a lot of grinding. The reason why there is so much is because you must constantly fuse your Digimon together to raise their level. Each time you do this they start over at level 1 and you must level them back up to 14+. I'll expand on this and talk about the formula later... For now all you need to know is when you get to level 14 on two Digimon it's best to DNA Digivolve them together.
Before we're able to continue with the game we must select a team, to do this visit the HQ you want and speak with the leader twice. Exit the leader's room and enter again, they will now recruit you. Your first mission will be to beat the boss in SCSI Domain.
Mission #2 & Learning The Game
When you dungeon crawl at this point in the game, EP is going to be a major issue. You'll have to use your Auto Pilot in the Menu to evacuate the dungeon each time you get low on EP otherwise you'll be paying 1000 Bits per crash out. You need your Bits to upgrade your total EP, recruit more Digimon and much more. So you don't really want to lose 1k each time.
For the second mission, my advice is to level up your Digimon. Once you get to level 6 - 10 you can progress to Mission #3 which is two dungeons for one mission. It won't take long for your Digi-Beetle to fill up with items, I personally recommend you vendor everything you get right now. We need to spend our Bits on two things primarily, Digi-Beetle upgrades and Gifts.
Tip!: After completing Mission #2 visit the Digimon Center and speak with the man inside. He'll give you a Toy Plane, this is a useful item that you should save for a bit until I tell you to use it. A TL;DR explanation of this item, it basically can be used to let any Digimon you fight join your team.
Tip #2!: Visit the Digimon Center each mission and talk with the Digimon Center Attendant. She will trade you one Digimon for another, this changes with each mission though so check back often!
To upgrade your Digi-Beetle go to the Main Gate area in town. Go into the room on the left here and speak with the guy at the far end of the room, he'll ask if he can work on your Digi-Beetle (pictured below). Tell him yes to enter into a new screen.
When you talk to this guy he will give you two options, Assemble and Upgrade. Assemble lets you add new pieces to your Digi-Beetle, for now choose Upgrade and max out the Crab BAT-1 item. Each rank you purchase for this will raise the max EP of your vehicle, 500 is the cap for this battery.
Our next important purchase is gifts which we use on Digimon to recruit them. You can purchase Gifts in your Tamer's Guild building, you should go with the rank D gift (the most expensive one you can buy right now) as this will give you the best chance to be successful. Recruiting new Digimon is very important since there is only so much we can do with our one person team.
This is also where the guild you chose at the start of the game plays a big role. You can only recruit Digimon that correspond to your own guild right now. For example, if you joined the Gold Hawks you can only recruit Vaccine Digimon. Blue Falcons are stuck with Data Digimon and Black Sword get Virus.
Gold Hawks: Vaccine Digimon
Blue Falcons: Data Digimon
Black Sword: Virus Digimon
You have one big exception to this rule though, some gifts work for all Digimon - like that Toy Plane I told you to get earlier. Also, like I said earlier once we get further into the game you can recruit any Digimon you want since you'll get access to all of the gift types.
Once you're ready to advance to Mission #3 talk with your Tamer Guild leader, you'll want to do this every time you beat a mission to advance the story. Mission #3 will unlock two new areas, Disk Domain and Video Domain. I'd recommend you spend some time getting 3 Digimon on your team before you complete these two locations.
In order to recruit a Digimon you'll need to press the Square Button when you see it on the overworld and use a Gift that you purchased on it (pictured below).Tip: If you don't see any of the items you purchased in the list it's because you need to go into the menu and Transfer them from the Server to the Digi-Beetle. It's tedious, but that's Digimon World 2!
There is one last important system for me to cover with you and that is the Digivolve and DNA Digivolve. You can do both of these things at the DNA Digivolve Operator in your Tamer's Guild, you'll find him in the room on the left. We'll be visiting this guy often as it's the only real way to make our Digimon more powerful.
Digivolve is something you can do at level 11, level 21 and level 31. At level 11 you can transform your Digimon into a Champion which will increase your stats and give you access to new Techniques which will deal more damage and cost more mana. You can also transform at levels 21 and 31 but they're far away for us right now.
Level 11: Champion Digimon
Level 21: Ultimate Digimon
Level 31: Mega Digimon
Something you may also notice is that your Digimon can't progress past level 13 initially. When you hit 13 your EXP to next level will be 99,999,999 -- even with codes the max EXP a Digimon can have is 9.9mil so you can never level past this cap without using DNA Digivolve.
DNA Digivolve is pretty straight forward, you will fuse two Digimon together and make a new Digimon which is capable of being more powerful than the previous two parents. Basically how it works is, when you fuse two Digimon together the new baby Digimon will have a higher EL capacity than the previous two parents.
Let's say for example, you have two Digimon who are level 13 and you fuse them together. 13 divided by 5 is 2.6 which is 2 when rounded down. This will mean your new Digimon has a max level cap of 15. You'll now need to level him up again to the new max level and then fuse him back down to level 1 again and again to increase his max level.
DNA Digivolve Math:
1. Take the EL of the two Digimon you're combining.
2. Divide the lower EL by 5 and round it down to the nearest whole number.
3. Add the result to the Digimon with the higher EL.
There is one more piece of this puzzle that I must explain and that is DP. Each time you DNA Digivolve you'll combine the DP of the Digimon you're fusing and increase it by 1. So for example, if you fuse a Digimon with 5 DP into one with 6 DP you'll end up with a 12 DP Digimon. Increasing DP is important because this will give you access to new Digivolutions for your Digimon. There is a secret Digivolution available to Digimon with 20 DP too, but that's going to be pretty time consuming to acquire.
Now you understand though why the game is so grindy, you must constantly level up 2 Digimon to max level then fuse them together which de-levels them. Then you must level again the new fusion and combine it again with another only to start over from level 1 yet again. You'll be repeating this process dozens of times because you need a team of 3 Digimon that are leveled up to beat harder content. It's not at all difficult to level up Digimon in this game, just excessively time consuming.
You can complete Disk Domain and Video Domain whenever you want. I'd recommend building out a team and then taking them out though, especially Disk Domain since it's much harder. At the end of Disk Domain make sure that you meet Angemon. One path leads to the Exit and another to Angemon. This meeting will unlock Meditation Dome which is a non-combat area to visit on the World Map.
Once you've finished both of the dungeons return to your HQ and talk with the leader. After, head over to the Tamer's Club and speak with Mark Schultz inside, he'll give you a Toy Plane and tell you about BIOS Domain.
Tip!: Spend some time grinding now! Catching Metal Greymon in the next dungeon is important and you need to be prepared to be successful!
Mission #3: BIOS Domain
Make sure you're prepared before going into this dungeon, there is a very noticeable jump in difficulty. There will be many fights where you are against two monsters that are levels 5+. Also, this is the dungeon where you will encounter Metal Greymon. He is a very powerful Digimon that I recommend you catch.
You will first see Metal Greymon early in this dungeon (pictured below). However, it isn't until later on the 6F that you can actually catch him. Metal Greymon is a level 21 Vaccine Digimon and you'll need to use the Toy Plane on him to have any chance of catching him.
It's important you avoid the 6F (boss floor) until you're ready to catch Metal Greymon. Once you exit the boss floor whether it be Auto Pilot or through the Exit pad, Metal Greymon will be permanently gone. If you're having trouble getting through this dungeon because you're running out of EP try upgrading your Digi-Beetle more or bringing some EP Pack-1 items with you.
DrillMiss1 is another item you can bring with you, it will allow you to destroy the rocks you find in the dungeon. Mag.Miss-1 will destroy the annoying Electro-Spores that damage you when you run into them. You'll start to encounter both of these things more and more as you adventure through the dungeons in this game.
To see the hidden traps you'll want to add some new parts to your Digi-Beetle, you can do that in the Main Gate at the Parts Vendor there. All of these parts are expensive which is the biggest downside... Visit Angemon at Meditation Dome if you haven't yet, he'll give you 2000 Bits for rescuing him.
When you feel you're ready, take out the boss in the BIOS Domain and then return to the leader of your HQ. They will give you an Entry Pass which lets you participate in the Coliseum and there will be a bit more dialogue that unfolds. For now, the item machines in the city will be broken and it's up to us to fix them. Most of the vendors will still work like normal but the item vendor will only sell EP Packs.
Missions #4 & #5: Drive Domain, Web Domain and Modem Domain
New Digimon Center Trade: Crabmon for Wizardmon
Some vendors in town broke, but others got a new inventory! Visit the Parts Vendor and Ammo Vendors in the Main Gate to check out their new items. LionEG-1 will give your Digi-Beetle more health, TurtleBAT1 will increase your total EP, Wasp RAM will let you carry and recruit one more Digimon and Crow BOX will let you hold double the items.
All of these items are important purchases, you'll want to buy one of each and then upgrade the ones that you can at the Digi-Beetle Mechanic nearby. If you'd like some story scenes, visit the Tamer's Club to meet a girl named Kim. You can also visit Angemon again in the Meditation Dome for more dialogue about Device Dome. Another thing I will bring up now is trades that are available during each mission. I put a tip earlier in the guide about this, but I will actually explain it a bit more now.
Many times when you get a new mission you can visit the Digimon Center and trade for a new Digimon. Speak with the Digimon Center Attendant (pictured above) and she will tell you what Digimon she wants and what you'll get in return. These trades are often a great way to get a higher EL Digimon and give you a bit less grinding to do.
When you are clearing Drive Domain there is a good chance you will run into your first Electro-Spore that blocks your route forward (pictured below). Depending on the RNG of how this dungeon spawns you may or may not encounter this on the second floor.
If you're lucky you'll find a Mag.Miss-1 inside of a chest nearby that lets you destroy this roadblock. Alternatively, you will need to purchase one of these at the Main Gate in town and bring it into the dungeon to use. I'd recommend bringing at least two with you because you'll often times find two spores that need to be destroyed along this route.
Tip!: If you run the same dungeon over and over it will eventually put you in different locations when you advance to the next floor(s). For example, you can skip the choke point you see in the picture below. The first few times you run the dungeon you always end up at this choke. Keep running it and you'll eventually start elsewhere.
Use Mag Missiles to destroy Electro-Spores
Complete both the Drive Domain and the Web Domain then return to your boss at HQ and talk with them. You'll need to visit Angemon next at Meditation Dome and speak with him to get your update. This will unlock a new location on the map, ModemDomain.
Our first objective is to enter Modem Domain and to beat the boss inside as well as Kim, this will unlock the Device Dome area. Be prepared for two fights when you go into this dungeon, the boss and Kim (both have 3 Champion Digimon). Visit the Device Dome after unlocking it and speak with Kim and her sister, you'll be given a Titanium Core as a reward.
This town has new vendors which you'll want to visit before leaving. You can purchase new Digi-Beetle upgrades and gifts for different Digimon than what your guild offers. For right now I recommend you purchase the Digi-Beetle upgrades since they're the most important. I bought PegasusEG1, Spider RAM and Crane BOX for right now. If you have the money, feel free to purchase a few more of the upgrades--otherwise save them for later.
Return to Digital City and outfit your Digi-Beetle with the new parts at the Digi-Beetle Mechanic (Main Gate). Don't forget to transfer them from your server after you buy them! While you're in this area you'll also want to speak with Chief Engineer Maestro. Assuming that you purchased the PegasusEG1, he'll upgrade your Digi-Beetle to a Titanium Body for free.
With all of that out of the way, return to your HQ and speak with the boss for 2000 Bits. Before we can do the next mission we'll have to visit the Coliseum and advance to Rank 3 (Rookie). This is very easy, it's just a couple of battles and is nothing you can't handle at this point in the game.
Once you've advanced to rank 3 return to the boss in your HQ and speak with them again. This will begin your next mission which is multiple dungeons in one.
Mission #6: SCSI Domain, Video Domain & Disk Domain
New Digimon Center Trade: Megadramon for Numemon
For this part of the game you're going to be getting a lot of Junk Parts in your inventory randomly when you pick up or use items. These items serve no purpose and can be discarded without any concern. You're getting them because during the story of the game at this time there are issues with items and the server. It's an annoying "feature" of the story.
You'll find a Blood Knight boss at the bottom of all 3 domains, Disk Domain will have two bosses. If you need to grind some levels I recommend SCSI Domain as that has many mobs. Another good piece of advice is to Run Away from battles, especially against the Numemon/Raremon combo packs. They're very annoying.
Once you clear all 3 dungeons return to your HQ and speak with the boss. After that head over to Device Dome and speak with Professor Piyotte (he's found in the top right room). If you need help finding his location use my picture below.
Piyotte asks you to catch 3 Digimon for him, Yanmamon, Syakomon and Ikkakumon. This part of the game is a bit of a pain in the butt if I am being honest. You'll need to buy a lot of gifts and get lucky to successfully catch these Digimon. Something you may not already know is you can feed the same Digimon multiple gifts before engaging it in battle. To have the best chance of catching a Digimon you'll want to make a red heart float above them.
Below are the locations you'll find the 3 Digimon that we need and the type of gift you'll want to bring:
Yanmamon: SCSI Domain 4F & 5F (Data)
Syakomon: Web Domain 5F (Virus)
Ikkakumon: Video Domain 5F (Vaccine)
In total you can give a Digimon 9 gifts before it will refuse any more. You may end up having it refuse some of those 9 gifts too, just keep force feeding until you get the red heart. My final tip to you is to defeat the Digimon you want to recruit last in the battle. Normally the last Digimon to be defeated is the one that will join your party.
Once you've captured all 3 return to Professor Piyotte and speak with him again. He'll tell you to find someone named Ben Oldman, this is a bit of a red herring and not something we need to do right now. You'll want to return to your HQ leader in town and speak with them. You'll get a scene after talking with your HQ leader about Digimon being infected and items going missing (we know that already thanks to the Junk Parts).
Return to Device Dome and speak with Piyotte again in the DNA Digivolve room (he's walking around). He'll ask you to collect 3 patches and return to him, two are found in Meditation Dome and the third is found in Device Dome. Before going to Meditation Dome buy and put a Digivice item in your inventory, you'll need this.
Speak with Angemon at Meditation Dome then talk with Clockmon in the room to the left. Give him the Digivice item and he'll give you a DATA Patch in return. Next, you'll want to speak with WereGarurumon in the other room, he'll ask you to meditate with him. Tell him you're tired after a bit of time and you will get the Vaccine Patch.
Last but not least, talk with Angemon and he will give you an update. Return to the Device Dome and speak with Kim again, she will give you the final item you need, Virus Patch. We have two people left to speak with, Professor Piyotte and our HQ leader back in Digital City. During your conversation with your HQ leader you'll learn about more Blood Knights.
Mission #7: BIOS Domain, Web Domain and Drive Domain
New Digimon Center Trade: Garurumon for MagnaAngemon
If you'd like to purchase new parts for your Digi-Beetle visit Device Dome, you can buy a GriffinEG1 and SharkBAT-1. These will increase your Digi-Beetle's EP and HP which will allow you to dungeon crawl for longer. At this point in the game I didn't really struggle for EP/HP though so the choice is yours if you want to buy them now or wait.
This whole mission is more or less dungeon crawling, the only tip I can give you for the dungeons is to bring some RetBugZap1 items. These will let you eliminate Return Bugs which are the really annoying bugs that send your Digimon back to the Server. An alternative fix to this is to fill your Server with 25 Digimon; this will make it so the Return Bug can't send anything back since it's full.
After completing all three dungeons return to your HQ and speak with the leader. This will get you a needed flag, head over to Device Dome next and speak with Kim. She will tell you to get her a Tankmon from the Web Domain dungeon. You can only find Tankmons on Web Domain 9F (the final floor) and they will come in a pack with other Digimon.
If you can't find a Tankmon, a Candlemon will work fine too--you'll just have to level it up and Digivolve into a Tankmon. You can find Candlemon in the BIOS Domain on the first few floors. These are easy to find and capture. Kim will give you an EXP Chip when you give her the Tankmon, return to your HQ in Digital City and speak with Lucky Luis. You'll get a X-Mech Part and your next mission.
Mission #8: Modem Domain
All in all this is a rather easy and straight forward mission. To complete the Modem Domain you'll need to beat 3 bosses in total, two of them are Joy Joy and Bertran. Once defeated they will return to town and wait for you, the final boss is a Blood Knight.
Return to Digital City and speak with Joy Joy in the Tamer's Room of your HQ. She will tell you where Ben Oldman is and unlock a new location on your map. Exit the Digital City and head over to Archive Port next, speak with Ben Oldman here to get your next task.
Missions #9 & #10: DVD Domain and Code Domain
The first thing you need to do is visit DVD Domain and defeat Ben Oldman; he is the only enemy in this entire dungeon. Defeat him then return to Archive Port again and speak with him again; once you do that return to your HQ in Digital City and speak with the boss tamer.
You will get a new mission which takes place in Code Domain. Much like the previous mission, it's a basic dungeon crawl with a boss at the end. After defeating the boss at the end of Code Domain return to your HQ and speak with the leader to advance the story again. You'll have to do this twice, the first time you show up you'll be send to another place, return again to talk with your leader.
Missions #11 & #12: Laser Domain & Power Domain
New Digimon Center Trade (After Laser Domain): Metal Mamemon for NiseDrimogemon
Our first dungeon for this part is Laser Domain. It's a pretty basic dungeon crawl, you'll probably need to bring a few Mag.Miss-3 items though which you can buy at Device Dome. You'll find the first boss for Laser Domain on the 11F, the other two bosses will be on the 12F. Defeating all 3 is required to complete the dungeon.
As always, once you're done the mission return to Digital City and speak with your HQ leader. Once that's done head over to Meditation Dome and speak with Angemon, he'll send you back to Leomon in Digital City next. You can find Leomon at the Coliseum, now is also a good time to level up more in the Coliseum if you'd like.
If you'd like to purchase some new items visit the item shop in Digital City, they have a few new things in stock. Also, Digital City has a few new parts that you can buy for your Digi-Beetle if you're interested. They are all minor/secondary parts though--none of them are major upgrades for your Digi-Beetle.
Next stop is the Digimon Center which is where you'll talk with Agumon a second time, he will give you the Ship Key item you're looking for. With this in hand you'll want to return to Archive Port and speak with Ben Oldman again, this will trigger a cutscene and open up an entirely new map for you.
For those of you out there who played Digimon World 1, the map above should look familiar. Enter into File City and speak with MasterTyrannomon, then hunt him down inside of PowerDomain which is the next dungeon. The dungeon is only two floors but the enemies are all pretty tough, just Run Away from as many battles as you can. Once you beat him you'll need to return to File City to continue with the story. To do this visit Archive Ship again and step into the teleporter, exit the new area and you'll be on the second world map (pictured above).
After speaking with MasterTyrannomon again you'll get full access to File City. You can purchase new items at the Item Shop and Digi-Beetle upgrades at the Digi-Beetle Factory across town. WyvernEG-1 is the new Engine, Mantis RAM will let you hold 7 Digimon and the Stork BOX allows 32 total items. There are a few more things you can purchase for your Digi-Beetle but you may not have the money for everything right now. The parts mentioned above are the ones you'll want to get first.
The vendor in File City also sells Toy Plane items which cost 8000 Bits each but they're the best all purpose Gifts you can get.
Mission #13: Diode Domain, Giga Domain, Port Domain & Scan Domain
When you enter Giga Domain you'll see that it's all dark, to fix this you will need the Electroder item which is found in one of the other dungeons. From my understanding which dungeon you get it in is random, but it will be one of the three. Once you have the item return to Techna-Dona inside of Device Dome to upgrade your Digi-Beetle's Radar to a Power Radar.
You'll find Jijimon inside of Giga Domain, once you defeat the final boss go into the room on the right and talk to him. Even if you rescue Jijimon before completing all 3 Domains, you'll still need to complete the third domain to continue the game. Once you've beaten all 3 and rescued Jijimon you'll return to him and speak with him again for the follow up mission.
Jijimon will also give you the Adamantium Core item. Take this item to Chief Maestro in Digital City to upgrade your Digi-Beetle again, you'll need the Dragon EG-1 item in order to complete the upgrade. You can buy this from Patamon in File City if you don't already have it.
There are a few other upgrades on Patamon too, you'll find him in the Digi-Beetle Factory. When you try to leave File City it will trigger a scene, a woman will appear in Jijimon's House and you'll have to visit them to advance the story.
Mission #14: Patch Domain, Mega Domain & Data Domain
New Digimon Center Trade: DarkTyrannomon for Myotismon
Back on the World Map you'll find 3 new dungeons, Data Domain will be the hardest one since it has multiple mandatory fights with friends along the way. Inside Data Domain you'll fight Bertran and Joy Joy on Floor 8, Mark Schultz, Debbie and Chris Conner on Floor 11 and finally Gekomon on Floor 14. In addition to all of these fights you'll also still have to beat the domain boss on Floor 15.
My advice for Data Domain is to go in and beat most of your friends, leave the dungeon to heal up then return. You can beat the final boss when you return to the dungeon. Once you've cleared all 3 dungeons return to Jijimon and speak with him again, there will be a short scene after which Soft Domain will be unlocked.
Mission #15: Soft Domain
You'll find Crimson on Floor 16 of Soft Domain, he is the first but not the only boss in this dungeon. After him you'll have numerous damaging floor tiles that you must run through, you're unlikely to make it through them all unless you bring about 5 MechFix-EX items with you.
The boss of Soft Domain is Chaos Lord, defeat him and then return to File City and speak with Jijimon again. It's time to return to the original map again, Digital City. We need to report everything that has happened to the leader of our team, doing this will unlock the next two dungeons.
After talking to your team leader you'll also update the vendor lists at Digital City and Device Dome. New items will be sold in Digital City and new parts can be found in Device Dome. I recommend you buy the best parts that you can afford. MammothEG1 is the best Engine, Hornet RAM is the best new RAM, Hawk BOX is the new item holder and GraviTIRES are the new tires. You should also buy the Orca BAT-1 if you didn't already get it from File City.
Once you're done purchasing upgrades it's time to visit Bug Domain and RAM Domain.
Mission #16: Bug Domain & RAM Domain
New Digimon Center Trade: Angewoman for Magnadramon
Both Bug Domain and RAM Domain will have multiple boss fights on different floors throughout the dungeon as well as a final boss (much like Data Domain in the previous missions). In Bug Domain you'll fight a Blood Knights Commander at Floors 7, 11 and 15 along with Commander Damien at Floor 17. For RAM Domain you'll fight a Blood Knights Commander at Floors 7 and 12 along with Commander Damien at Floor 17.
These two dungeons are where I really started to notice a spike in the annoyance level when exploring the domains. Many dungeons will have Return Bug Nests in them which will send your Digimon back to the Server. You can prevent this from happening by capturing enough Digimon that you fill the Server... Or you can carry RetBugZap3 items (these are purchased in Device Dome).
You'll find many other obstacles along the way, rooms filled with traps that you must disarm to continue. I recommend you bring missiles and repair kits too (for repairing broken parts) when you dungeon dive. You don't want to reach Floor 15 and be unable to progress because a part is broken!
Once both dungeons are beaten return to Digital City and go to the Main Gate, you'll have a scene with Commander Damien. Next, follow him to the Coliseum for another scene and then finally to the Tamer's Club. Once the long scene is finished return to the team leader and report all the details, this will unlock the next mission.
Mission #17: ROM Domain
To beat ROM Domain you'll need to bring some Mag.Miss-5 items to get rid of the red Electro-Spore; you can purchase these items from Device Dome. I recommend you bring at least 5 Mag.Miss-5 items and 5 MechFix-EX items with you when you do this dungeon. 5 is more than you need but it will cover any situations that you may run into.
Once you have beaten ROM Domain you'll need to report back to your team leader at the HQ. If you haven't been keeping up with battles at the Coliseum you'll be told to go visit there and to achieve Chief Tamer (Rank 9). After you do that, return to your HQ and speak with your team leader, you'll have a scene involving all three team leaders when you do.
Mission #18: Core Tower
New Digimon Center Trade: MetalGarurumon for MetalSeadramon
New items are for sale in your HQ and you can make a new trade at the Digimon Center. When you're ready to advance the game head over to Shuttle Port on the Directory Continent and watch the scene. You will regain control of your character on a new map called Kernel Zone--the only dungeon here is Core Tower which is our next stop.
Core Tower is a pretty straight forward dungeon, work your way down to Floor 24 and you'll meet the guardian, she changes based on who you chose as your team leader at the start of the game. After the scene with her is done you'll exit the dungeon like normal and be sent back to File City.
Mission #19 (Final Mission): Chaos Tower
Our final dungeon of the game gets an anticlimactic start, simply return to Kernel Zone and go into the new dungeon. This tower is only 20 floors and resembles Core Tower a lot, the first few floors can be annoying but it gets linear really quick. Bring some Mag.Miss-5 items because you'll likely find some Electro-spores blocking your route. Much like the previous dungeons work your way to the bottom and defeat the boss.
Your boss this time is Overlord GAIA, the first fight against her will be just her. The second fight will involve two arms that assist her throughout; I recommend using your AoE attacks that hit all opponents on the second fight to dispatch the arms. All in all, I found this to be a rather easy ending boss.
Defeating Overlord GAIA will get you a cutscene and the credits will roll. However, this isn't the end of the game just yet. Press Start to skip the credits if you want and you'll end up back in File City (pictured below).
There will be a long scene in File City, when it's done return to the Main Gate and talk with the New GAIA. New GAIA will let you take the Digi-Beetle out again to visit the new bonus dungeon, Tera Domain. Like many bonus dungeons, this is 99 Floors in total and you should expect to deal with a lot of annoying mechanics.
Before you try this dungeon you'll want to fill your server with Digimon to negate Return Bug Nests. You can also fill your Digi-Beetle to negate Memory Bugs too but this isn't as necessary. As far as items to bring, I recommend the following (at minimum) to deal with the annoying mechanics:
15-20 Mag.Miss-5
5-10 Parts Fix
5 EP Pack-3
Depending on the Digimon you're using, you may want to bring restorative items for them too. Although, I seriously recommend you run from almost every fight along the way. Your reward for beating this dungeon will be the best Digi-Beetle Parts in the game, MaximusEG, WhaleBAT, EagleBOX and BeetleRAM. All of these items are found on Floor 99.
You can also find unique and rare Digimon along the way, if you're interested in expanding your team even further. There are many guides online which will list Digimon floor by floor in this dungeon, such as this one on Gamefaq. If you manage to beat this dungeon, congrats! You've not only beaten one slog of a game but you've also conquered the bonus dungeon too!