It's good to get The Calibrator side mission out of the way. A: because it's easy, and B: because it's right by the following main mission. Head to the waypoint inside the office, and hit the button behind the picture frame to activate the elevator. Once you're in, walk up the stairs to trigger the cutscene.

Only Jensen would have to sneak around his own headquarters. He has to plant the whisper chip inside The Collective. The door to the room you need to gain access to is locked. Fortunately, there's a vent system that leads right into it. The access to the vent is to the right of the locked door. Follow the vent into the room.

The door inside that room has too high of a security rating. Jump up to the ledge on the left and open the hatch on the grate you're walking on to get around it. Find the server at the end of the hallway and plant the whisper chip. Then go and talk to Miller to trigger the next cutscene.