Welcome to the Mirror Universe. Captain Spock of the Terran Empire has captured the U.S.S. Enterprise and taken Commander Spock captive. Meanwhile, Captain Kirk of the Federation has found an uneasy ally in the peaceful Augment Singh, a man Kirk knows better as the violent Khan. Together Kirk and Singh travel to Qo'noS, where they encounter Kirk's own surprising doppelganger...
James T. Kirk takes perverse pleasure in seeing himself from the outside before commenting how unusual it is to see Leonard McCoy with two eyes. Seeing his Terran counterpart puts to rest any doubts Kirk had about being in other reality before K'Hav and Nyota Uhura deduce the ion storm resulted in the USS Enterprise crossing over. K'Hav has been tracking the ion storm but given the unpredictable nature of such phenomena, it is liable to disappear as suddenly as it appeared and as the last recorded sighting was in the 22nd century, the storm may not reappear until the 24th century. The two Kirks agree to work together to get their ships back, though purely out of circumstance.
On Vulcan, Captain Spock has brought Spock to Amanda Grayson. Or rather her grave. Grayson was a traitor to the Terran Empire and was summarily executed. The fact that she was given a grave at all is hope to Spock that is counterpart is not completely heartless only for the captain to reveal the grave was given only at Sarek's request. Captain Spock has never considered his mother anything but an embarrassment.
Aboard the SS Botany Bay, Captain Kirk is briefed by his counterpart on the circumstances via which he lost the ISS Enterprise to Spock before revealing he acquired the ship after murdering Christopher Pike. Before Kirk can attack his counterpart, the Botany Bay arrives at Vulcan under cloak and undetectable to the ISS Enterprise. After Captain Kirk makes clear he will not tolerate his counterpart killing anyone, the group beams aboard the Terran flagship. Captain Spock and Uhura have but a second to gape before Kirk shoots Spock through the head, killing him on the spot reminding Captain Kirk that he never actually agreed to the no-killing rule. Spock then applies the Vulcan nerve pinch to Uhura before Kirk, in accordance with Terran law, proudly retakes command of the ISS Enterprise.
Though Kirk is ready to honor his word and help his Federation counterpart find his Enterprise, it suddenly drops out of warp directly in front of them, now commanded by "Keptin" Pavel Chekov. As Kirk tries to get Pavel to surrender the Enterprise, the young Russian is promptly killed via injection by Leonard McCoy who begs to be beamed off the depressingly clean Federation ship. The instant the Federation crew is back aboard, Kirk orders the shields raised, rightly suspecting his Terran self saw them as easy prey. The USS Enterprise attempts to set course for the ion storm but the Terran Kirk orders his ship to attack before his own ship is attacked by the SS Botany Bay. Singh hails Kirk, both men finally agreeing to be allies, and telling Kirk to find the ion storm before cutting the line. With no options, Kirk orders a course set for the storm.
The Enterprise made back to their universe with seconds to spare. In his ready room, Kirk asks Spock if he thinks Singh survived. Given the state of the Botany Bay and the considerable armament of the Constitution-class, especially given the Terran upgrades and a bloodthirsty captain...no. It is highly unlikely Singh survived. Kirk concedes but hopes they will never encounter the other reality again as he contemplates the spectre of his Terran counterpart.