The Staff was stolen by Manchester Black from the DEO. He then contacted J'onn through their mental link telling him to meet him in his father's grave. It is there he used the staff to set fire around M'yrnn J'onzz desecrating it also using the staff to slow down time to hold Supergirl at bay. It was there he had a conversation with J'onn telling him that their mental link worked both ways and he was going to punish J'onn for betraying his martin manhunter roots in accordance with the sacred scriptures of Mars.
He then fled getting ready to enact the punishment before he did he tormented J'onn mentally while he was trying to use the mental link to find him. Showing the dead forms of Alex and Kara showing him that we lose everything if he continued his path of peace one of the visions strangled him. However, it was J'onn strangeling himself until he was snapped out of it by Kara. J'onn, fed up with all that Manchester has done, realizing he would never stop with his vengeance, and not return to the man he was before Fiona's death, J'onn took the Staff of H'ronmeer and aimed it at Manchester, turning him into energy and absorbing him into the staff killing him. Manchester merely stood still and smiled telling J'onn he was beautiful. 
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