Bullseye had joined the Masters of Evil and was a member of the assault force that attacked the Helicarrier, leading a group of Ultron Drones to the base's missile systems. Nick Fury sent the Ultimate Alliance to stop the missiles from launching, but Lester managed to fire one of the missiles at New York City anyway. The Ultimate Alliance, including Daredevil and Elektra, battled and defeated Bullseye, taking the missile control keys from his unconscious body and disabled the bomb. Bullseye was then taken into S.H.I.E.L.D. custody.
During the Superhuman Civil War, Bullseye had nanites implanted in him, turning him into a Pro-Registration soldier. Bullseye fought in many battles, and helped Venom and Green Goblin destroy the Geffen-Meyer Chemical Plant. He later helped the Green Goblin detonate a bomb to distract the two sides fighting in the Negative Zone Prison so Moonstone could attack Iron Man. Bullseye was one of the founding members of the Fold, and was battled in the prison by the reunited Ultimate Alliance. He was freed when the Nanite Nick Fury was defeated and the signal was shut down.
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