Ellis was an agent recruited by Benton to the agency, he belonged to Gabriel Logan's convoy in Kabul in Afghanistan as a demolitions expert. After that he worked for the agency until his death in Costa Rica. While Ellis was not very good at gunfighting, he had unshakable loyalty, as he chose to die rather than revealing information about 'The Agency' to Rhoemer, who interrogated him.
Ellis, full name unlisted, was an operative of the Agency in 1999 assigned to the investigation of terrorist Erich Rhoemer. Prior to that he served as a member of the U.S. Army and specialized in demolitions. During his time, Ellis participated in an escort mission to help a CIA convoy deliver weapons to Arab rebels during the Soviet invasion of Afghanistan.
An assault by the same rebels reduced the unit to Ellis and Gabriel Logan. Both men worked in conjuction with Edward Benton believing him to be a CIA officer. Their transport of the weapons to Kabul ended with Benton trying to supply the Soviets with the arms and showing his allegiance to the Agency.
Ellis and Logan became operatives at a later date, and Ellis worked undercover in Costa Rica to examine Erich Rhoemer's connection to narcotics growth. Rhoemer was then working for the Agency and exposed Ellis, holding him hostage and cutting off his communication. He commanded Mara Aramov to execute Ellis before the arrival of Gabriel Logan and Lian Xing.
Ellis just appears in the introduction, he was acting as an undercover agent in Rhoemer's plantation in Costa Rica. He was discovered and Rhoemer ordered Mara Aramov execute him. When she killed him, Gabe and Lian heard the shot and found Ellis dead.
Syphon Filter 3
" We're being flanked! "
-Ellis in CONVOY mission
He appears in the second mission in Costa Rica (he just appears in his death scene) and he appears in the mission CONVOY in Kabul, Afghanistan as the demolitions expert for Logan's convoy. In this mission, the player -who takes control of Logan- must provide protection for Ellis, while the latter uses explosives to open the way and defuse the mine scattered on the road.