After the Attorney General heard a recording of President Logan incriminating himself in the death of David Palmer and other crimes, he alerted men on the ground at Logan's eulogy for Palmer to take him into custody. When federal marshalHoltzman demonstrated to Logan that he had unknowingly been wearing a microtransmitter, and that he was under arrest, Logan demanded that Agent Clarke arrest Holtzman. Instead, Clarke assisted with the arrest of Logan. ("Day 5: 6:00am-7:00am")
Logan: Agent Clarke, arrest these men, and get them the hell out of here.
Clarke: I'm sorry Mr. President, we have our orders.