Flit has become an insane maniac whose spent his life obsessed with building bigger and stronger weapons to destroy the UE and kill every last one of them. With control of the Federation Fleet he's lost his humanity and eventually becomes a major villain of the series.
Wolf has become the leader of the rebel army that doesn't trust the ever growing evil federation and after breaking Grodek out and re-uniting the crew of the Diva snoops further and further into Federation's dark secrets, eventually teaming up with a faction of the Martians that are trying to find a peaceful resolution to the on-going war.
something something SEED/Star Wars/etc...