Season 2: Doomsday Saga
Episode 1: Enterprising Young Men
After Lieutenant Kirk's true identity is revealed to Slezak and Kor, they are promptly rescued by Captain Christopher Pike of the brand new Starship Enterprise, which is leading the Starfleet Armada towards Organia. Kirk and Slezak attempt to convince Pike to call off the attack and work towards an armistice instead, but Pike is less than receptive and throws them both in the brig leaving Spock to be only one he will listen to. The crew of Grace try to negotiate with Kor showing him that his occupation is a fraud orchestrated by Commander Chang and his war mongering houses.
Episode 2: What Dreams May Come
After the ordeal on Organia, Kirk is named Captain of the Enterprise as to the last will and testament of Christopher Pike. The crew head to the pleasure planet Risa only to find it is has been destroyed by some great and powerful force. Marisa's Starfleet news feeds indicate other solar systems have been destroyed in a straight path from the Ceti Alpha System. Rob keeps having nightmares of Organia; the memory of killing Chang with his own sword is especially vivid in his mind, but he keeps it from his friends and fiance.
Episode 3: The Secret Origins of Khan Noonien Singh
After Ceti Alpha V is destroyed by a planet killing super weapon, Khan finds himself captive by the crew. One-by-one they visit him in the brig getting bits and pieces of his true history. Khan recognizes Rob's Post Traumatic Stress and drives a wedge between him and his friends. The crew set a course to pursue the Planet Killer under the control of one of Khan's genetically enhanced supermen named Malik.
Episode 4: Counting Stars
After Malik kills Khan and names himself leader of the Augments, Grace is left heavily damaged by his Planet Killer and they come across the wrecked Starship Constellation and begin salvaging spare parts. The crew becomes aware of Rob's PTSD and relieve him of command leaving the equally traumatized Commodore Decker to seize control of Grace and pursue the Planet Killer on a suicide revenge mission.
Episode 5: The Right Ship for the Right Job
After Decker's failed attempt at revenge, Slezak regains command, he decides to call for help from Captain Kirk and the Enterprise in stopping Malik and the Planet Killer from destroying yet another solar system. Dom and Aiden recruit Mr. Spock in a secret plan of theirs that could stop the Planet Killer, but still risk an entire solar system's destruction at the same time.
Episode 6: The Needs of the Many
With Malik dead, the Planet Killer is now free to destroy any solar system it wants making it even more dangerous. Dom, Aiden and Spock are close to completing their secret project to build a trilithium torpedo meant to trigger a super nova that could destroy the Planet Killer, and when Rob and Kirk catch wind of this, they are both outraged, but agree that they may have to sacrifice the lives of millions to save trillions.