Vaughn had created an alliance between himself and the Cybermen and planned an invasion of Earth in exchange for power. Vaughn however intended to betray the Cybermen once the they had invaded Earth.
When he met the Doctor and Jamie McCrimmon, Vaughn was told by the Cyber Planner that one of the Doctor's pieces of circuitry came from his time travel machine. Vaughn planned to use this as insurance to escape with his security chief, Packer.
Before Vaughn could betray them, the Cybermen betrayed him and his plans began to crumble. He allied himself with the Doctor to defeat the Cybermen but was killed by them in the process.