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Sounds like you haven’t finished that quest… the discord group has a lot of tips and guides for all the various quests I’d recommend joining if you need help since most don’t really tell you how to complete them even I can’t remember 100% but I will try,  I think at the part you’re at you need to talk to some of the digimon in the village who mention him training hard then find him again in the sewers (I think) where you fight again. 

Story spoilers below:

After you beat Black Agumon again he gets mad runs off, talk to the villagers again who will mention he has turned into a black Metalgreymon and is attacking people then he attacks Server City (which is a big town), you are asked to go save the city which after you do it unlocks and you can start fixing buildings and recruiting a lot more Digimon including Meramon. 

Have you done the Big Koromon/Black Agumon Quest? 

Aka, Have you unlocked the Server city map? 

If you’ve reached the level & training cap then you can’t do much else with that digimon other than give it better equipment or apply status effects to attacks. 

If you’re really invested you could try the ReBorn mechanic but I haven’t tried it myself so I can’t really give any pointers. 

Otherwise just keep it as a favourite in the box and build another digimon. 

Wish I could toss all those random digimon I’ve collected into a meat grinder and get exp that way. 

Yes all 3 can be recruited.

For Betamon I believe you have to catch a certain amount of fish

For the other two you'll first have to do the giant Koromon/Black Agumon quest line and then the requirements are below.

Nanimon: 5K wins and all challenges completed

Meramon: Clear Fire Mastery : Endurance I and II challenge

If they sing click them, If they get the angry speech bubble click them, if they have the scribbles in a speech bubble use the soccer ball. 

Every Digimon also has a favourite food (and hated food), Friendship goes up a decent amount feeding them their favorite food (The icon will get a star next to it when you find it's favourite)

Later in the game after you recruit more digimon to the city there are some food you can cook that will increase friendship easily.

I heard it's best to starve them if you want to reborn.

Have to help Medicmon so he builds a hospital in server city which then sells the item.  He appeared in the Drive Savanna for me and asked for 20 Digiherb, Rainbow Soup and something else with a 2 hour time-limit. Rainbow soup is cooked by the bird digimon in server city so you'll probably need that unlocked before he appears.

I agree each species needs it's own high level area like Aquatic & Dragons do, best way I've found to get other species exp is to refresh the challenges until you get a challenge that has the species exp you need at the right level, it's still tedious but if your monster can complete it itself you can basically afk it while watching youtube.

Last option in the in the "Digivice" Menu

You can switch it in the options menu

How nice that Blue Wormmon got a little bit of his power back, I had no idea I had broken the game when I decided to feed the funny blue worm a cake, after that it pretty much unlocked every area for me in v1.0.0, he is now immortalized forever in my storage.

For windows the save is stored locally on your PC, you can delete the replace the .exe without losing anything

I sent some love and put some Rick Astley lyrics in there. Good luck egg.

Only taking queens and dodging everything else to find the flag seemed to work well for me, It's an interesting concept putting two things I enjoy together and I think it could shine if it had a bit more polish. 

Plus chess has really blown up lately.

This is easily one of my favorites I've played so far, love the idea, design and the boss theme that won't leave my head. Would love to see this expanded further if you ever decide to do that.

If I had to criticise anything it's that I think the characters are Too Willing to do the correct thing, I would have made them a little more stupid but I think that'd be an interesting way to implement difficulty settings just make the AI more suicidal.

Great idea and execution, wish it was longer and had more unique dialog to certain phrases eg. "Your Tasty", had me laughing.