He was guarding the Second Doctor and Jamie McCrimmon in the medical bay when Kemel Rudkin was killed. When Jamie went to the door and tried to investigate, Flannigan told them they couldn't come out of the medical bay.
He encountered Elton Laleham and Armand Vallance after their space-walk but didn't know they were being controlled by the Cybermen. Vallance tried to kill Flannigan but accidentally shot and killed Laleham instead. Flannigan was then hypnotised by the Cybermen.