He is the son of Allen O' Neil who became a soldier much like his father. Seeking revenge on the Peregrine Falcon Squad, Allen Jr. joined with the remaining soldiers of the Rebel Army and infiltrated a remote island used by the PF Squad as a training camp for new soldiers. Disguising himself as one of their drill instructors, he led many of the PF soldiers into the island, who were then captured.
Two PF recruits, Walter Ryan and Tyra Elson, fought against the Rebel forces on the island, so Allen Jr. led them into a trap, making them fall into an underground cavern inhabited by the island's natives. The two escape and continue on their mission, fighting through the Rebel occupied areas and reaching the core of the island, where Allen Jr. set a machine to create earthquakes, apparently intending to sink the whole island. The two recruits fight against Allen Jr. and defeat him, then destroy his machine thus saving the island.
Allen Jr. fights much like his father, jumping around, shooting from his machine gun and throwing grenades. Once he loses some health, he drops the machine gun and draws his combat knife, now pursuing the player to slash him.