The second film in the X-Men chronology is actually the seventh X-film that was made, and boy, does it know it, as it pulls in practically every character to have ever starred in an X-Men film up until this point. It's a little tricky to peg down this film to one particular point in time — it opens in the year 2023, following a group of mutants last seen in 2006's The Last Stand, including Charles Xavier and Erik Lehnsherr, now played by Sirs Patrick Stewart and Ian McKellen, reprising their roles from the original trilogy. However, the setup is just an excuse to send Wolverine's (Hugh Jackman) consciousness back to his younger body in 1973, where he must stop an assassination in order to prevent a future in which mutants are hunted to the point of extinction by deadly machines called Sentinels.
There, Wolverine attempts to enlist the help of the younger Charles and Erik, but they have conflicting ideas for how to prevent the disastrous events of the future and very nearly wind up destroying each other in the process. Ultimately, though, Wolverine's mission is successful, and his consciousness returns to 2023 to find that not only did he prevent the rise of the Sentinels, but he also managed to undo the events of The Last Stand, which resulted in the deaths of Cyclops and Jean Grey. In this new, warmly lit future, Cyclops and Jean are alive and well, Xavier's School For Gifted Youngsters is intact and thriving, and none of the apocalyptic events we saw at the beginning of the film ever happened.
However, this shoving of the timeline onto a different track does make things a little weird when it comes to the films that were made before it, but chronologically take place after it, which brings us to . . .