Since Raph’s whole situation is reminiscent of 2k3′s Good Genes Arc... is it possible the team will have to cooperate with a villain to get the resources they need to cure Raph?

It’d probably be the Kraang, since they’ve got advanced technology and are the source of the empyrean in the first place. They’re also pretty likely to double-cross the team, so the team will be able to defeat them and not have to deal with any long-term consequences from cooperating with them.

On the other hand, if they have to cooperate with the Council of Heads or members of the human government, then perhaps there will be long-term consequences, which we could see play out should we be so fortunate as to get a Season 3.