Flanigan hates his younger brother due to his childhood sweetheart marrying him instead. He also has regular sexual fantasies involving Major Esmerelda Ndoci (the unit's CO) and chocolate sauce.
It was during the war between the Confederacy and the zerg that, while serving in E Company of the Annihilators, Flanigan was heavily involved in anti-zerg operations, only to be recalled to Tarsonis to help recover a rogue telepath for the Ghost Program, at the same time the Sons of Korhal was heading for Tarsonis.
Along with Ghost Program wrangler Malcolm Kelerchian, Flanigan and the rest of the unit were dispatched to the southwestern district of Tarsonis City, intending on retrieving their subject from the headquarters of crime lord Fagin. Due to orders from General Ledbetter, the plan was accelerated, Flanigan and E Company storming the compound.
The mission was a success, though Flanigan soon found himself dealing with the zerg on Tarsonis and the replacement of the Confederacy with the Terran Dominion. To this end, he has retained his place in the unit, which now serves in the Dominion Marine Corps.
Flanigan may have been promoted to sergeant, as in mid 2500 he was studying for his sergeant's exam.