Emilia is going to continue recruiting humans for her “reverse the mutes” cause. Meanwhile, Kipo will continue to recruit humans and mutes for her “humans and mutes live in harmony” cause. She already has some mutes on her side, and given that she saved several enemy mutes in the finale, I think they’re going to side with her. (Newton Wolves redemption!) If nothing else, they may want to unite against a common enemy. She’ll make a plea to the Clover Burrow people and will probably get at least some to join her. Kipo will make an effort to show her people the wonders of the surface world.

You know the blonde guy from Clover Burrow, one of the higher ups? I think he’ll be a significant figure in season 3. There’s also a young girl seen with him (she looks like him, and is presumably his daughter) who has a pretty distinct design. I think she’s going to be a significant character too.

Scarlemagne gets a long term redemption arc. He’ll have to do something big and life-risking to prove to the characters (especially Kipo) that he’s changed.

Dr. Emilia creates the anti-mutagen. She tests it on some mutes and we see them become normal animals, and it’s super fucked up. Kipo Squad has to stop her from releasing it into the environment. Hugo’s redemption could come in here: she tries to use the anti-mutagen on Kipo or another character, but Hugo takes that bullet. They re-mute him later of course.

Dr. Emilia infuses mute genes into some of her supporters so she can use them as weapons.