When S.H.I.E.L.D. was decommissioned and its agents auto-transferred to the newly founded H.A.M.M.E.R. during the Dark Reign storyline, Eric remained with H.A.M.M.E.R. This was despite the fact that 1200 agents who were Fury loyalists (including Dum Dum Dugan and Gabriel Jones) resigned and formed the Howling Commandos PMC. It later transpired that he was working for them from within, and aided in a heist that saw the HCPMC (now owned by Fury) raid a number of H.A.M.M.E.R. Helicarriers, and bolstering their ranks when over 3000 H.A.M.M.E.R. agents defected to their side. He is later killed in a battle against HYDRA. Gabriel Jones is also one of the many S.H.I.E.L.D. fatalities along with Eric.
Eric Koenig appears in the Agents of S.H.I.E.L.D. episode "Providence" played by Patton Oswalt. Reviewer Oliver Sava called Koenig "a breath of fresh air after all the tense events leading up to his appearance". He is a worker at Nick Fury's secret S.H.I.E.L.D. base Providence. Eric Koenig has Phil Coulson keep private about the fact that Nick Fury is still alive. In "The Only Light in the Darkness", Eric Koenig conducts lie-detector tests on Phil Coulson's team in order to see who can be trusted. When it came to Grant Ward, Eric Koenig had to do some follow-up questions to him which he answered correctly. He is asphyxiated offscreen by Grant Ward and his body is found in the ventilation by Skye. In the episode "Nothing Personal", Eric Koenig's body was found by Jemma Simmons, who confirmed Eric Koenig's cause of death. Oswalt returned in the season finale "Beginning of the End" as Billy Koenig, who oversees the S.H.I.E.L.D. secret base the Playground.