By 2379, he held the rank of Lieutenant, an served as a security officer aboard the USS Enterprise-E. In that year, he was part of the Delta team under the command of Lieutenant Christine Vale which was sent to Tezwa's Nokalana Sea to destroy the nadion-pulse cannon firebase located there underwater, since he had taken deep-dive training.
Before transferring to the Enterprise, Fillion washed out of Starfleet Special Ops training. Christine Vale hypothesized that Fillion's habit of making smart remarks in response to being given orders was likely a key factor in this, even though he was smart and cool under fire. (TNG novel: A Time to Kill)
On Tezwa, Fillion was part of the mission that captured General Gyero Minza, the head of the resistance. With three punches, Fillion was able to knock out and capture Minza. He couldn't wait to get home to Mars to tell his son Jason that "he got to beat up a general with his bare hands."
A short time later, Fillion was on the runabout Tunguska headed for Alkam-Zar when the Loyalists began their final assault. The runabout was hit from the ground and crashed with only Fillion and Ensign Fiona McEwan surviving. Fillion was killed by the attacking Tezwan ground troops and only small portions of his body could be recovered as McEwan detonated a photon grenade to prevent the Loyalists from capturing them and the runabout. (TNG novel: A Time to Heal)