Yeah, I'm kinda surprised that they didn't have Storm show up in this episode of X-Men '97. I though for sure that they were setting up her return in...
I guess this would be the equivalent of Marvel's close to long decade of mediocrity in their cartoons (just compare X-Men '97 to Avengers Assemble)
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The team knew he wasn't dead though? They saw him get taken into space by Lilandra. I guess they could be upset thinking he was living the high life...