What didn't people understand about it? I thought it was fairly simple. All of the members of the Hellfire Club, including Cassandra Nova, weren't real. Emma used her psychic powers to make people think they were there. Emma drove Cyclops crazy and then attacked the other X-Men and wiped Beast and Wolverine's, so Kitty stuck her in a hole in the ground. The fake Hellfire Club members kept fighting her. Then, Emma made Kitty remember three years that didn't happen, where she had a son who the other X-men imprisoned, so Kitty brought Nova's body out of the box and passed out. While she and Colossus were unconscious, Cassandra told Emma to transfer her (Cassandra's) mind into Kitty's body. However, Cyclops shot the fake Emma to make her disappear, because it wasn't the real Emma, it was a mental projection. After she and Colossus woke up, Kitty went and fetched the real Emma from the hole in the ground.
Cyclops explained that Cassandra planted a piece of herself in Emma's brain, a psychic command that would drive Emma crazy and make her rescue her body. While Cyclops was talking, Emma hallucinated that Cassandra was talking to her and no one else could see her (like Six and Gaius Baltar). Kitty wanted to kill Emma but didn't. While the X-men were talking, Emma started to transfer the mind of Cassandra from the Stuff body to the body of the new student (the one who could project armor around herself). Then Danger and Ord broke in and SWORD beamed them all up to their spaceship. All the X-men definitely got taken, and I think Ord and Danger, but I'm not sure about the Stuff-body and the new student.
I'm kind of shell-shocked from the issue-I can't decide whether I love it or I hate it. I guess I'll have to wait and see where it goes.