X-Men: The New Beginning
The gist is that the school returns to normal after the events of the Last Stand, with Storm, Beast, and Logan becoming the teachers. However, Logan tends to just up and leave quite a bit, so they decide to bring in a new teacher, a Ms. Emma Frost. I'd stick with her Ultimate version, where she was a teacher of another school like Xaiver's in Chicago, and someone Charles had talked about in the past (I wouldn't bring up the Hellfire Club at all in this movie).
Bobby, Kitty, Colossus, Rogue, and Angel are still students, but in the senior class and are becoming mentors to the younger students.
We learn that the cure isn't as permanent as they thought as Rogue has begun to re-gain her powers even before the movie begins and the mutant communitty is aware of it. But because Bobby and Rogue were together for quite some time while she was "normal", Kitty and Peter had become an item (to please all the fanboys).
However, with Rogue's powers coming back, it's putting a bigger strain on hers and Bobby's relationship, and they decide it better to take some time off for a while.
One night during the beginning of the movie, a knock/buzz (whatever) is heard at the front door of the school. When they answer it, we see two people (a man and woman) standing close together (we can tell they're a couple), and the man just says, "Hello, my name is Alex Summers, I've come looking for information regarding my brother." (or something along those lines) We find out that the girl with him is none other than Lorna Dane, aka Polaris.
The X-Men are shocked to find out that Scott had a brother, but soon find out that the professor had kept it a secret from them after looking into his Cerebro files. Alex states that someone contacted him and told him to come to the Xavier School for answers. We learn that Alex and Lorna were in another country (probably Genosha) doing some kind of refugee work for years in the middle of nowhere to escape the life of being a mutant and persecution.
Of course they let him know that Scott is presumed dead as Jean had killed him up at Alkali Lake, but Alex isn't too keen on that idea since there's no body and no evidence except for his glasses which Logan recovered.
Meanwhile, there are reports in the news about a number of mutants suddenly disappearing from their homes, most of them appear to be homeless or poor, aka The Morlocks (or Omega Muties as seen in X3). At first no one thinks anything of it, but then as Storm and Rogue are out in the city, they are tracked down by Callisto (she ain't dead from what I saw in X3) and confronted, but not to fight. Callisto tracks down Ororo to ask for help regarding the missing mutants.
Rogue notices another person with Callisto, looking to keep an eye out for something, and as he turns to look at her, his red eyes startle her. Yeah, it's Gambit. Nooch. We come to find out that he's relatively new to the Morlocks and Callisto is a bit weary of him since he showed up.
Cut back to the Mansion and to a new Danger Room session, except this one doesn't suck. This time we get full Sentinels and more students in the DR. A 5 to 8 minute special fx showcase of all their powers.
Now of couse since the Cure didn't work, that means Mystique and Magneto are now repowered, but weak. Magneto has reformed his Brotherhood, Juggernaut, Pyro, Multiple Man, and Sabretooth. Since the humans don't know the cure doesn't really work, Mystique is easily able to escape her captures by inpersonating someone since they're not expecting it. We can just assume Pyro and Juggernaut escaped with the crowd ala Magneto at the end of X3.
Magneto also hears of the disappearing mutants and assumes it's the US government taking them to do experiments on them for another cure. But this time, instead of trying to just march in and kill everyone, he sends Pyro back to the school to fake like he wants to return and be on the good side once again. This way, he has a mole in the school and can gather intel on what the X-Men know about the situation. Pryo is welcomed back, but of course Bobby and Rogue are weary of letting him back in.
Emma with the help of Callisto try to locate the missing mutants with the help of Cerebra (had to throw Emma in this movie to provide the X-Men with a psychic and she'll be used much more in the later movies). What they find shocks them. One of the newly missing mutants is seen being carried away by none other than Gambit himself. Callisto is furious with this traitor and vows to kill him herself. Emma suggests that they just follow him to see where he's been taking the Morlocks.
Storm, Bobby, Rogue, and Callisto follow Gambit to some side entrance of what appears to be a run down facility on the out-skirts of New York. He knocks, and is let in, as he enters, he looks around and Rogue catches him looking over at her behind some cover, but he does nothing and enters the building instead.
The X-Men break into the building and don't find anything out of the ordinary until Callisto senses Gambit and someone else below them. They find an entrance to some sort of underground lab full of viles, equipment, beakers, mad scientist type stuff. During their search, they don't realize that they're being watched and out of nowhere Gambit and some weird looking mutants attack them. We are let known that they are former Morlocks, but have been grossley mutated and/or tested on.
Huge fight scene ensues, the only thing of importance here is that Gambit and Rogue square off and/or she steals his powers for a bit. Callisto and Bobby get injured so they must retreat back to the Mansion.
Back at the School, Pyro gets ahold of the knowledge of what happened and where the facility is and reports it back to Magneto. Once Eric hears of this, he seems to put it all together and figure it out. He utters, "Essex.." We get some backstory on Dr. Nathaniel Essex, though Eric did not know him personally, he is aware of his brash experiments and unusual methods. He says that Charles once met with him a long time ago to discuss the evolution of the mutant gene. He believed him to be dead many years ago.
Because Rogue absorbed some of Gambit's powers and memories, Emma tries to read her mind to obtain more information about him, his name, where he's from, just what his powers can do, etc. They both get the sense that he's confused and might be under some sort of manipulation. We can tell that Rogue is feeling sorry for him and has began to start to fall for him.
Pryo lets the X-Men know that Magneto is back and planning to attack (insert something here), so the whole team gears up ready for a fight, but when they get to the place, there's nothing going on. Instead we see Eric, Sabretooth, Maddrox, Juggernaut, and Mystique waiting. They needed to meet in a private place to talk about the going's on with Essex. Asking Eric how he knew about what was up, Mystique morphs into Gambit to let them know she has ways to gain information as well, it's also let loose that Pyro was just a spy the whole time.
While the X-Men are away, Beast, Bobby, Emma, Havok, and Polaris are back at the Mansion when the entire place is assaulted by grotesque mutants with increased strength and powers. The remaining X-Men are out numbered and too weak to withstand the assault and are defeated. When they awake, they're still at the mansion, but notice that Alex and Lorna are gone.
They call for other team members for help and alert them of the situation. Once Magneto finds out that the mansion was attacked, he laughs it off, but then hears that Alex and Lorna were taken, and his mood suddenly shifts. He tells the X-Men that one more time, they need to put their differences aside and confront Essex once and for all.
So now the final battle begins. The Brotherhood and X-Men (minus Bobby and Emma) arrive at the facility. Juggernaut and Colossus make waste to the front entrance very easily and clear a path for the remaining teams. They pair off and split up to search for the missing mutants. (Now we can get some great dialogue and backstory here by teaming up Logan and Sabretooth, Colossus and Kitty, Storm, Rogue, and Mystique, Beast and Magneto, Angel and Pyro, Juggs and Multiple Man)
Fight ensues, yadda yadda yadda, Gambit is there along with some throw away cameos for lesser mutants and morlocks. Rogue decides to take on Gambit again, but this time Rogue grabs powers from all the different mutants so she's a total bad ass and just kicks everyone's ass. During the fight, Gambit gets knocked back and something either breaks or falls out of his coat/head gear thingy and he appears confused and weak. They realize it was some sort of mind control device, thus letting Gambit turn good once he sees that he was being used by Essex. They find Havok and Polaris still alive and barely conscious and free them. Of course they still get a few shots in now and again. Magneto seems especially happy to see Polaris in good health and while helping her escape it's revieled that she is his daughter. Magneto could say something along the line of, "You think that all my time on this planet and I haven't had the time to father children?", "Children" being the key word. Lets us know Wanda and Pietro are out there.
Near the end of the battle, Essex finally reveils himself in some grand fashion sort of way but calls himself Mr. Sinister now. He looks nothing at all like Eric remembers him, he now has pale white skin, dark black hair, red eyes, and seems to be in top physical shape for a man that should be in his 70's let alone dead. Either he lets us know, or it's revealed some other way that the reason he's been kidnapping the mutants to perform experiments on them was so that he could isolate a specific mutant gene. Unfortunatly, none of the Morlocks possessed that gene so he turned them into mindless killing machines. He also lets the audience know that he already got what he needed from Lorna.
Then he mentions to Alex that what he obtained from him, was something even more special. Alex has had enough of this and just blasts Sinister with his powers, and all hell breaks loose. The other "morlocks" awake and fight off the x-men/brotherhood while the whole place is coming down. Fires erupt and explosions are going off everywhere. The X-Men are forced to retreat and the Brotherhood takes off as well.
We cut back to the Mansion where things are explained and Havok and Polaris decide to stay until Alex finds his brother, but can't help but wonder why they were abducted in the first place. They wonder what Sinister meant by "what he obtained". Lorna must now also deal with the fact that she now knows who her real father is. Gambit is also now with the team and he and Rogue seem to have some tension between them as she still feels uneasy around him. Bobby notices this and tries to talk to Rogue about it, but she just denies it. The Gambit/Rogue saga would continue into the next movie, I think it'd be too early to just make them a couple in this movie without actually getting know eachother first.
Credits Roll...
After credits, we cut to a dark room where we can see make out a figure in a cloak talking to what appears to be himself. We recognize it to be Sinister's voice and he says something along the lines of, "Yes my lord, I have obtained what is needed for you. No, they will not be a problem anymore. I.. I hope you do not mind, but I also obtained a sample for my own project..." And as he says this, we pan over to see a tube with some sort of human like figure in it, and the name, "Scott Summers" on a name plate. "Yes lord, the APOCALYPSE will be upon us!"
End
(Not EMMA) Jean? Or madelyne? ... just curious. 
