Allen directs the Intelligence Division of the World Ninja Association (WNA) and stands as a primary antagonist. He orchestrates covert operations targeting individuals aware of Ninja-Gum's secrets—Burton, Berecca, Ron, and Jane—specifically for their knowledge of the gum's side effects and research data.

His ambition is to militarize Ninja-Gum, securing global dominance for Komerika. To advance this goal, Allen partners with Harold Cook, Komerika's president, offering political support in exchange for access to the gum. Allen later betrays Harold, deliberately withholding critical information about the gum's adult-de-aging side effect. When Harold learns the truth from Burton—who demonstrates the transformation—Allen leverages his knowledge of Harold's illicit rise to power to block retaliation.

Allen expands his reach by allying with Luke, also known as Master Shadow, leader of the Shadow Ninjas. Together, they stage attacks using Space Ninjas to sow chaos in Eagle City. This manipulation aims to position the Shadow Ninjas as protectors, enabling a takeover under martial law. For their endgame, Allen and Luke conspire to launch a nuclear strike on Eagle City. Luke uses puppetry to seize control of Harold, forcing him to authorize the strike under the false pretense of saving civilians, intending to eliminate the city's population while framing Harold. Ron and Jane later free Harold from control, averting the attack and exposing Luke's manipulation.

Throughout these events, Allen consistently exploits his institutional power within the WNA. His motivations center on consolidating authority and eliminating perceived threats through assassination, manipulation of political figures, and large-scale destructive operations.