This topic has been discussed in a number of threads in some form or another so I thought I'd create a single thread to focus on this issue. At the moment, it's the biggest mystery of the post-Secret Wars re-launch. What happened to Cyclops? What exactly were the "terrible acts committed by mutant revolutionary Cyclops" that put mutants in the crosshairs? Exactly what is the extent of the "damage" he's done? Is he even alive after the 8-month gap? And what happened between him and the Inhumans?
These are all pressing questions. The answers are essential to the setup of the X-books after Secret Wars. We've already seen a preview of Extraordinary X-men #1 where O5 Jean laments what happened to him. We also have seen on the covers of All-New X-men depictions of the O5 team crossing out pictures of Cyclops' revolutionary team. So what does this mean? Well, that's what I'd like to discuss here in this thread. And I also want to open it up to any speculation and/or theories about what happened.
Now I've made my share of predictions before. Almost every time, I've been dead wrong. I am not Rich Johnson. I have no insight whatsoever. I'm just assessing the situation as is currently understood. So with that in mind, don't put much stock into anything I try and predict. I'm almost always wrong.
That said, I do have a couple theories about what happened after Secret Wars. Here's the theory and I think is most likely.
Inhuman/X-men War Theory
During the 8 month gap proceeding Secret Wars, a major skirmish erupts between the Inhumans and Cyclops' revolutionaries. It happens when a new form of the Terrigen Mist, which was already hinted at in the pages of Ms. Marvel #18, is unleashed from New Attilan. Based on the EXM #1 preview, we already know it causes disease and sterilization in mutants. As soon as Cyclops finds this out, he confronts Black Bolt and urges him to stop it. Black Bolt refuses, claiming that they would be denied an entire generation of Inhumans.
As a result, a major war erupts and Cyclops unleashes his Sentinels on New Attilan in the hopes of stopping the mists. The Inhumans fight back and during the conflict, more of the mist is released. So in the end, Cyclops and his team fails. This forces Cyclops and his team to retreat. In the process, Cyclops is detained again by the Inhumans and turned over to the Avengers. As a result, he's relegated to a SHIELD holding cell. And to ensure that further conflict between mutants and Inhumans doesn't continue, Beast offers to join the Inhumans in finding a cure for the effects of the mist.
For the mutants who are affected, the remaining X-men under Storm create a save haven in space for mutants and regularly shuttle them to this haven. It was recently revealed Alpha Flight is on some kind of space station with Captain Marvel. Perhaps this is where mutants are being sheltered until the mists are dealt with.
In addition to the effects, the spread of the mists causes more Inhumans to emerge. Plus, the attacks by Cyclops give mutants an even worse public image. He's already a revolutionary who has openly defied humans. This would heighten anti-mutant sentiment. And it could inspire the O5 team to set out on their own to help repair that image.
As I said, this is the theory I think is most likely. However, my prediction rate is pitiful so this might get debunked by the time New York Comic Con rolls around or even before, depending on new solicits.
I do have other theories, one of which involves Cyclops dying or becoming terminally ill in this Inhuman/mutant war. But for now I think this is the one I'm sticking with. If anyone has other theories they want to share or discuss, I think they're worth discussing. We'll find out soon enough, but there's still plenty of time to speculate.