The teams clash without having any real dispute, it's just their usual setting for interaction. The Mutants end up taking Bird Boy home: we'll find out more about him later. But that's calling that the A-plot is like saying whatever scientific expedition the Enterprise is on that week is automatically the A-plot.
What this issue is actually about is Magma, who Claremont spent so much time setting up and then has mostly ignored. She's far more foreign than anyone else there, having grown up in a culture that was completely isolated from the "modern world", even by reputation. But in practice she's not been the one who has been getting the culture shock, and beyond a rivalry (if you can call it that) with Selene and being handy in a fight may as well not have been there.
She's had a letter from her dad saying that her letters have been very useful but that she should come back home now. She likes Empath of the Hellions (this was teased a bit in #53-#54), and she wonders whether she wouldn't be treated better at the Mass Acad. So, assuming that Emma's offer is still open, she decides to transfer. Perhaps she's thinking that'll keep her dad happy. All a bit sudden, though. And that Selene, she's still Black Queen. Has she thought about this much?