I think that is the episode where they also go deep into Christianity. Where Nighcrawler talks about his faith as a mutant and talks about scripture, God, faith (its pretty much a Church sermon) and Wolverine argues that he use to believe in God but doesn't because God allows mutants to suffer. Then at end of the episode Wolverine seemingly comes around to the faith and is seen praying in a church. Also, the episode has a line with Rouge questioning things and it also heavily implies that Gambit is an atheist. While I am a Christian myself, I am shocked something that was so religion focused was allowed on a mainstream Saturday morning Marvel cartoon in the 90s with no controversy. That would NEVER air in 2021 that's for sure.
But I believe the clip is still on Youtube if anyone is curious.