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Near the end of the movie, Manheim is reassigned, by order of CIA Deputy Director Ward Abbott, to kill Conklin because of Conklin's failure to apprehend Bourne.
Manheim's fate is unknown, as he was the only one of the three assets that Bourne didn't kill, though in The Bourne Supremacy, former Treadstone operative Jarda tells Bourne that they are the last two Treadstone agents, implying that Manheim died of some other cause during the span between Identity and Supremacy.