He was the canine military officer in charge of F.O.W.L.'s so-called psychic division. He was originally in command of F.O.W.L.'s military until an incident in which he marched several troops (presumably Eggmen) to their deaths in an erupting volcano in an attempt to secure it for unknown reasons. Synapse detested his newfound position because he wanted to command disciplined troops while the psychic division's only other members, a pair of hippies, were the exact opposite. Using an unnamed device Synapse and his hippie sidekicks tracked psychic vibrations to Dr. Sara Bellum's secret S.H.U.S.H. laboratory in the Swiss Alps.
There, Synapse offered the hippies as test subjects for Dr. Bellum's invention, the Norma Ray. They eventually stole the device, and Synapse used it to give the hippies psychic powers, after which they adopted the super-villain identities of "Hotshot" and "Flygirl." After defeating and capturing Darkwing Duck, Synapse and his "troops" returned with him to their hideout, encasing him inside a giant icecube. Synapse planned to dispose of Darkwing by having Flygirl drop a "duck smasher" (a giant anvil) onto him, but ransomed the hero's death to F.O.W.L. High Command, making a variety of inane demands, including his own personal parking space for his tank.
This delay resulted in Darkwing's rescue by Gosalyn Mallard and Launchpad McQuack. After Hotshot and Flygirl were defeated, Synapse used the Norma Ray on himself in the hopes of growing smarter and figuring out a way to defeat Darkwing. He overdid it however, evolving into a being of pure thought, a disembodied head with a giant brain.
In this form, he was nearly indestructible. However, Darkwing turned the Norma Ray onto him while he, Gosalyn, and Launchpad asked Synapse rapid-fire questions, causing the giant brain to think during the blasting process (a big no-no) and explode, killing Synapse.