This is Robert Kirkman’s run which had its ups and downs, although he did have an overall arc in mind since the beginning.
He starts with a few issues focusing on relationships within the team. Scott and Jean, Rogue and Iceman, Logan and Ororo, Kurt and Alison, Kitty and Peter Parker, and he also introduces Lilandra, which continues the Phoenix mythology started by Millar.
That’s explored even more in the next arc (69-71) when it’s clear that the Phoenix is not a legend and it’s not created by Jean’s mind. Although the characters don’t know yet. Meanwhile Magician is the new member of the team, and he helps fight the Brotherhood. Kurt keeps being unhappy about Piotr’s sexual life, and confesses his love for the comatose Alison.
The next arc (72-74) finalyl reveals the truth about Magician, which was a nice twist. He didn’t even realize his powers, and when he did it was too late. The end was heartbreaking and lonely, but it was the only one he could allow, other than suicide.
The second annual sees Nightcrawler kidnapping Alison after she wakes up from her coma. This behaviour has been planted by Kirkman since the beginning, with Kurt growing ever more frustrated due to Piotr and Alison/Angel.
Issue 75 starts the main plot in this run, with the introduction of Cable. I like that Cable is now Wolverine from the future, it’s less convoluted than the 616 version and it’s easy to understand and justify. He also appears to be a villain (with Bishop as his enemy), since he kills Xavier, the first time Xavier “dies” in the ultimate universe. However it turns out that Xavier is alive and in the future, where Cable is preparing him for a big battle, while Bishop was always working with Cable but stuck in the present. Meanwhile Scott disbands the X-Men and turns the school into a pacifist haven for mutants.
Beast is brought back in issue 81, while Mystyque is now out and working with Magneto. The Morlocks are introduced, just in time for Nightcrawler to join them. Bishop recruits mutants to effectively substitute the X-Men. I like that Alison turns out to be a much more powerful mutant than she even knew.
In 84-88 the Sentinels are back, and it turns out that Fenris are behind them this time. Styfe is also introduced, though he turned out to be a spineless selfish man. Even Trask has a better ending than he does.
Issue 89 seems ties up a few storylines before the big final arc. Wolverine finally kills Cornelius, and Storm fights the Shadow King. This actually felt too rushed, as if Kirkman didn’t have much time anymore, and he had to close those threads in a hurry. Not only that, but there was one big thread that he couldn’t close: Magneto. Now we know that was because of plans for Ultimatum.
His final arc sees the return of Sinister, who manages to achieve his goal: release Apocalypse. There’s a huge battle, with many victims (Angel, Bishop) and in the end Cable brings back Xavier all suited up (looking like Onslaught) ready to defeat Apocalypse… except he can’t. It all comes down to Jean and Phoenix, who merge and defeat Apocalypse.
She also changes reality to before this all happened.
Throughout his run Kirkman tried to develop the characters and their relationships, while at the same time introduce new concepts and continuing previous threads. Unfortunately the ending felt very rushed, and the big concept of Cable preparing Xavier in the future felt like a moot point. He was also not helped by the continuing change of artists, and their low quality compared to previous ones. This is probably the weakest run on the series so far, which is a shame because I think Kirkman had some good ideas.