 When Marcus arrives aboard Vengeance and attacks Enterprise , Kirk and Khan work together to take control of Vengeance 's bridge . Once in control of Vengeance , Khan kills Admiral Marcus and demands that Spock return his crew . Spock , having removed Khan 's people from the torpedoes , lowers the Enterprise 's shields and allows Khan to beam the activated weapons ' warheads aboard Vengeance , crippling the ship . Khan crashes Vengeance in San Francisco in an attempt to escape , but is pursued and captured by Spock . Khan is placed back into cryogenic sleep along with his crew . 
