Following the events of the film Star Trek: First Contact, the Enterprise, while returning to the 24th century, is diverted to the 20th century of a parallel universe by a powerful time traveler called Kang the Conqueror. There, they encounter the super-powered mutants named the X-Men, and assist them in fighting Kang's plan to remake the timelines of every known universe. If these two groups of heroes fail – history itself will change forever!

On the planet Xhaldia, ordinary men and women are mutating into bizarre creatures with extraordinary powers. But is this a momentous evolutionary leap or an unparalleled catastrophe? The very fabric of Xhaldian society is threatened as fear and prejudice divide the transformed from their own kin. Dispatched to cope with the growing crisis, Captain Picard and the crew of the Starship Enterprise receive some unexpected visitors from another reality, in the form of a group of mutant heroes known as the uncanny X\-Men. Storm, leader of the team, offers her help in resolving a situation that is agonizingly similar to the human/mutant conflicts of their own time and space. But when hostile aliens appear in orbit around Xhaldia to try and abduct the transformed for use as superpowered weapons in an attack on the Federation, even the combined forces of the crew of Starfleet and the X\-Men may be unable to prevent an inferno of death and destruction. Starfleet's finest crew and Earth's greatest mutant heroes will need all their powers and abilities to save the Xhaldia people and stop a deadly threat to the Federation.