Colonel James Harper is a corrupt colonel that works for a sinister science division called Project Cadmus who was also best friends with Hank Henshaw.
Jim was brought in to deal with J'onn J'onzz infiltration of the D.E.O.. Jim along with Lucy Lane were there to clean up the agency. The two take J'onn still in the form of Hank Henshaw to a interrogation room that is so alien proof that Supergirl could not listen in.
During the interrogation J'onn told the two about what happened ten years earlier in Peru, when he befriended Jeremiah Danvers, which began with the real Hank Henshaw leading a manhunt for a alien who he believed was dangerous. Jeremiah tried to protect J'onn which ultimately lead to the death of the real Hank Henshaw.
However, Jim, who was close friends with Hank, as well as having a hatred for aliens for no apparent reason, doesn't believe him and is placed in custody. J'onn told Alex Danvers she was next, and likewise is grilled by Lucy and Jim. She explained how J'onn as "Hank" approached her to join the D.E.O. after she was arrested after a DUI, saying that she was special, and that she owed it to her father to be the person he knew she could be. Alex even passes her lie detector test, but Lucy doesn't believe her. After Kara discovers earphones so she can listen in, she is stunned that Lucy and Jim are taking the two to Project Cadmus.
After a moment of clarity, Lucy agreed to help Kara. Later that night, as the vehicle is en route, they are surrounded by motorcycles that throw the truck off course. One of the cyclists is Supergirl, who disarms the guards, while the other cyclist, Lucy, help Alex and J'onn escape, but not before J'onn erases Harper's memory of having remembered meeting him, but discovers that Harper now remember that Danvers is alive at Cadmus.