It opens with Xavier being revealed to be alive still, but in a coma. With a guest Hulk appearance, they figure out a way to revive him. It doesn't look particularly like they knew this would be the last issue, although the gratuitousness of the guest appearance could be read as a last desperate attempt at achieving more sales. The only textual reference to this being the final issue is a small caption at the bottom-right of the last panel. "And they fought happily ever after... ??" I came to this hoping to see a more successful X-Men vs Frankenstein story than X-Men #40, and it is, but only because that issue was such a failure at that.
There's not much resolution. We never do see how the new status quo of the seven X-Men and Xavier work. In fact, Alex and Lorna are still not really properly part of the field team (they are left to guard Xavier), and neither have codenames. Poor Bobby is really not dealing well with his crush on Lorna. He's calling her "his girl", despite her clearly being into Alex. Alex isn't dealing that well with it either, ending up in a fight with Bobby.
In issue #544 (which is not a bad issue number to get to in the first volume of a series that was originally cancelled after #66), Gillen has Bobby compare the original five to the Beatles. He's not wrong, if you go by the dates, although that's been obscured by the sliding timeline. Emerged bursting into pop culture in 1963, broke up in 1970. Never quite the same again, even when they reunited years later (posthumously for the Beatles, postnatally for Cyclops).