As the Enterprise prepares to test the Genesis device in orbit around a desolate planet, they encounter a small pod containing a mentally unstable, bipolar remnant of the Eugenics War (Khan, played by Johnny Depp). Khan is having an internal struggle trying to control the murderous and malevolent emotions resulting from his incomplete genetic engineering.
Kirk befriends Khan throughout the movie as he sees elements of Khan in himself (no real father, misunderstood). Certain personnel in Starfleet place pressure on the Enterprise to get the test underway. Khan appears to have a psychotic break and steals the Genesis Device and beams down onto the planet, killing Kirk's fiance aboard the Enterprise in the process. A frenetic cat-and-mouse chase ensues as Kirk personally chases down Khan in one of the planet's labrynthic cave networks. Khan's genetically superior half seems to gain the upper hand on him, giving him the upper edge in the chase and setting traps that nearly kill Kirk until they finally meet. A vicious physical battle follows in which Kirk, out for revenge, strangles Khan to the point of death. Khan manages to fight Kirk off and escape, with Kirk in pursuit.
Meanwhile, on the Enterprise, Spock discovers why Starfleet has been placing so much pressure on them to begin the test. In one of the planet's many underground caves, a secret dumping point exists for the genetically altered descendants of the Eugenics Wars.
Kirk, notified by Spock, realizes that violence is not the solution in this situation and tries to get through to Khan. The better side of Khan manages to break through for an instant, allowing Kirk to catch up, but not before the Genesis device is activated from a remote source. Kirk confesses to Khan that Khan killed his fiance. Spock realizes that Starfleet is using the Enterprise as a relay point to control the Genesis device and that the only way to stop the device from being used in this murderous capacity is to place the Genesis device on the Enterprise, travel away to an empty part of space, and then destroy the Enterprise. With precious few minutes remaining, Spock sets the ship for autopilot and sends a shuttle to bring the Genesis device onboard. Khan, filled with guilt, incapacitates Kirk at the shuttle site after everyone has taken refuge, boards the shuttle and maroons himself onboard the Enterprise with the Genesis device. With his last breath, he apologizes to Kirk on the empty bridge as the Enterprise self-destructs, destroying the Genesis device with it.
The movie ends with Kirk realizing that one of the descendants on the planet is Khan's son. Kirk adopts him as his own. Spock faces a court martial from Starfleet as the crew realize this conspiracy runs deeper than initially thought.
OK, that's pretty fanboyish.
