X-Factor - this iteration of it anyway - had to end like this. The original premise was the five of them reunited again to fight mutant problems in New York City. Along the way they lost their original shtick of being fake mutant hunters and in its place acquired a fuck-off massive spaceship in the city.
Now that the X-Men are gathering again, now that the construction crews in Westchester are readying their pencils and inks, we have no place for Ship. Fortunately Ship came with its own kill switch. It came by way of Apocalypse, and X-Factor have never satisfactorily understood it. It is this vulnerable to a large storyline involving him. But it has to be a big story - perhaps his biggest - if we are to have such a big status quo change as a result. The way it sort of manages that is by throwing crossovers at the page. First Avengers (briefly) and then, more substantially, the Inhumans.
Ah, the Inhumans. Again, a major part of the Marvel cosmogony that we are only talking about as we get to the 1990s. If they have crossed over with the X-Men before it had been in other pages. Our exposition on them comes courtesy of Beast, who would have worked with them before (perhaps fought them) during his time on the Avengers. Beast's time on the Avengers has been somewhat of an ignored point as far as this series goes - but then, X-Factor has always been a contradiction. A team of renegade outlaws funded by a well-connected millionaire, and staffed by said millionaire, a respected former member of the most important superhero team, an accountant, and a woman who had been brought back from the dead by the collective efforts of not just the Avengers and the Fantastic Four. They've had their losses - Angel in particular, but this is a team of winners who have been befallen by circumstances, not the bunch of misfits that X-Men wants to be.
The Inhumans are what the X-Men tend towards. Whereas Cyclops acts like the king of the mutants (with Jean his Red Queen), the Inhumans are explicitly led by their monarch, Black Bolt or, to give him his full name, Blackagar Boltagon (that never gets old). Like the mutants the Inhumans are humans plus: in the case of the mutants this arises spontaneously (or so we think). For the Inhumans it is a combination of long-ago genetic manipulation by the Kree, combined with activation by the terrigen mist. There are other differences. The Inhumans are a race, a distinct group, as opposed to the distributed minority that the mutants form. The Inhumans have a royal family formed by blood, whereas the X-Men are the ultimate in found family.
In this story, the X-Men are trying to make a transition to blood family. This is in the form of Baby X, Nathan Christopher, the son son of Cyclops (in truth) and Marvel Girl (in spirit if not in literal truth). If he is raised to adulthood without major trauma they have succeeded. But also at that point the X-Men is if not over them certainly then this generation of characters are no longer usable in the same way. This is something the X-books are still not ready to do, even in 2014, although they are perhaps the closest of all of Marvel's line to allowing it.
Scott's eventual assumption of the role he had pretended to take in the X-Terminators is many years down the line, but we can see the seed of it here, as Baby X, who had been terminally infected by Apocalypse, is taken into the future to survive. Coming to it over twenty years later, we know he'll become Cable, and he'll raise another child in the future in turn, who will return as a messiah. None of this is planned yet (well, perhaps Cable=Baby X), but the story is very forward-looking. The last dialogue spoken in #68 (other than by the Watcher), is by Scott, to Charlotte Jones:
You're wrong, sergeant. It hurts. It always will. More than I could put words to. But the dream that bound us all together - X-Factor and before us the X-Men - was based on hope.(their emphasis) Hope is coming.