open the game and open the level "origins" (the second one) or just play through the intro to get there. In brians lab grab the green keycard and open the door that requires a green keycard. Now go back to the normal level path and play all the way to the fire vents. In the fire vents you will find a room with a pool of water in it. In the water there is a blue keycard. Now backtrack to the start of the level at brians lab (the sealed door should open if you are in possession of the blue keycard). Go back to the door you open with the green keycard and open the second door where he awaits.

pick him up and put him on your face/head and ignore the message written in blood because nothing happens when you take him to the surface.

Note: your wearable brian is sensitive and must be kept well fed with the blood of your enemies.