When the Doctor and Jamie McCrimmon met with Bob Hall on 20 July 1966, Kennedy monitored their conversation as part of Waterfield's plan. He met up with Hall and told him that the Doctor and Jamie had followed him there. When Hall baulked at kidnapping, Kennedy knocked him unconscious and left clues for the Doctor to follow. Later after he reported to Waterfield, he became curious about what Waterfield was up to.
After a bit of searching, he found Waterfield's secret room. While he was trying to break into a safe in that room, a Dalek materialised on a time machine in the room. When Kennedy noticed it, he tried to run, but the Dalek exterminated him. (TV: The Evil of the Daleks)
Zoe Heriot saw the moment of Kennedy's death on the TARDIS scanner when the Doctor used a telepathic projector to show her the kind of monsters she would be up against if she joined him and Jamie on their travels. (TV: The Wheel in Space)