First off: SPOILERS AHEAD
Second off: This is (mostly) just for humor purposes. I know some stuff is a stretch, but it's all part of the fun.
An officer in a elite intergalatic force commits an atrocity that kills many people, only to be headed off and forced to flee by a young upstart hero. The officer flees into the depths of space. To hunt him down, the hero is put in command of the most advanced spaceship in the fleet, trying to follow in the footsteps of his mentor, the ship's original captain. The hero and his crew hunt down and engage the officer, only to learn from him of an even more pressing threat. This threat comes in the form of a massive, powerful warship they have no hope of defeating conventionally. But, using knowledge from a old, wise source, they are able to destroy it, as the heroes hunt down and defeat the officer as he attempts to use the ship to destroy the elite organization's intergalatic headquarters. But the hero's ship is torn to pieces by a massive ship, and during the destruction the hero makes a sacrifice play to save his crew, and dies.The hero is later brought back from death by very illogical means, given an upgraded version of his destroyed ship, and sent on a mission into deep space.
Is it Star Trek: Into Darkness, or Mass Effect?
I don't even know anymore.