Mikhail pops up in the moon pool of The Looking Glass. He thought Bonnie and Greta were on assignment in Canada and they say that Ben didn't want anyone to know they were down there. Mikhail goes to talk to Ben, who gives him orders to kill Charlie and Bonnie and Greta. He walks out and shoots Greta. Bonnie runs and he shoots her in the back, but doesn't kill her. Before he can shoot again, Desmond shoots him with a spear gun.
Episode 3x22, Through the Looking Glass