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By 2267, Chekov was serving on the ISS Enterprise under the command of Captain James T. Kirk. In that year Kirk, Scotty, McCoy, and Uhura of that universe switched places with their prime reality counterparts after a fruitless attempt by Kirk to force the Halkans to provide them with dilithium.
Chekov was ordered by Spock to commence with preparations to issue the standard response, so he and Sulu began entering calculations to destroy Halka. When the prime universe James T. Kirk arrived on the bridge Chekov sensed right away that something was off about Kirk, which was confirmed when Kirk ordered the Enterprise not to fire on Halka.
Signalling his men Chekov followed Kirk into the turbolift. After arriving at their destination Kirk found Chekov's men waiting for him, and Chekov about ready to deliver the coup de grace. Before Chekov could vaporize Kirk, one of Chekov's men turned against him and knocked him out and vaporized the remainder of Chekov's men with his own phaser. The remainder of Kirk's men soon arrived and asked Kirk if Chekov should be put in the booth. Not realizing what that meant, Kirk gave his assent.
A short time later Kirk learned what his men had meant when they asked about putting Chekov in the booth, when Kirk happened to walk past the booth while talking to mirror Spock. After finishing his conversation with Spock, he ordered Chekov be removed from the booth and confined to quarters.
This act of mercy raised Spock's suspicions even more, and Spock quickly figured out that a transposition had taken place. Soon after with assistance from the respective Spocks of both universes, the transposed people returned to their home universes.
After the Mirror Universe version of Kirk returned to his home universe, he had learned what Chekov had done. He ordered that Chekov be returned to the Agony Booth, but the power be turned down on the booth. 13 days later, the desiccated corpse of Chekov was removed from the booth. A photograph of Chekov's corpse was taken by Kirk, which was framed. After becoming Emperor Tiberius hung a copy of this photo at his hideout in Iowa.
In the game Shattered Universe, Chekov was still alive in 2293. By then he held the rank of Commander and was in command of the ISS Enterprise-A.