The first issue (by Fred Van Lente and Andrea Di Vito) is set right between #138 and #139, and depicts Kitty's first mission. She's been sent by Xavier with Wolverine to investigate a new blip on Cerebro. Wolverine protests, and it's only by Xavier blackmailing him by threatening to withhold help in recovering Wolverine's suppressed memories (something that in fact had not been introduced into the comic yet) that he goes along with it. This is all bit arbitrary by Xavier, and while he is a bit of a reckless bastard at this point, I'm not sure I believe it.
The scenes on the plane journey are amusingly awkward. This is Kitty's first time in her costume, and she isn't sure whether to pick "Phantom Girl" or "Phase" as a codename. In West Virginia, they quickly track down Michelle, whose mutant ability had been causing trouble, and suggest that she could attend the school.
That's the problem with this story set here, of course. Michelle will get sent to Muir Island and pops up again in #6, but there she disappears from continuity entirely. Presumably she gets depowered on M-Day? Who knows?