Strange behavior by Emma Frost displayed in earlier issues is explained in this storyline. It seems that many years ago, Cassandra Nova was responsible for Emma’s secondary mutation–diamond-hard skin.
In exchange for this power, Frost agreed to spy on the X-Men from within. Nova then buried that memory until now, when she wakes up her sleeper agent, which explains why Emma has been behaving underhandedly in the background ever since Joss Whedon started writing this book.
Frost then begins mental attacks, causing frightening delusions for the cast and quite literally mind-F-ing Scott while dressed as Phoenix–and turning Scott into Wolverine.
As for the real Wolverine, he becomes a cowardly idiot. Beast goes feral. Stuff like that.
The drama continues to ratchet upwards until Kitty figures it out…
That’s a tribute panel.
She then attacks Emma, phases her deep into an underground cavern, and essentially buries her alive.
The main side story, though, is SWORD and SHIELD trying to negotiate jurisdiction over an alien attack as Ord returns from Breakworld and demands that Earth turn over the recently resurrected Colossus, and we get to see Armor in action.
It comes together in the end. They temporarily neutralize the Ord/Danger threat, while Kitty and Cyclops take down Cassandra Nova.
Cyclops has to use a gun, by the way, because Emma’s psychic meddling caused him to lose his powers.
He recognizes that Emma was being manipulated, and forgives her for all she has done.
Emma throws Nova’s influence off.
What they don’t know is that Nova has “downloaded” herself into Armor, and will emerge later.
At this point, Ord and Danger break free, attack, and everyone is teleported into a SWORD rocket and sent to Breakworld.
Blindfold, the precognitive, predicts that not all of them will return.
There’s also lots of great smaller storylines, like Wolverine training the newer students, Kitty and Peter re-starting their relationship, etc. I love this series. It’s one of my all-time favorite runs on X-Men.