After you encounter all 3 androids, when you transport out to TSA, prime reality is restored and you are messaged by Baldwin (the normal one). Sinclair's involvement to all this has been proven, and he orders you to try to find him, promising to contact you as soon as he has some information on his current whereabouts.
Exit the Pegasus, stand back, go to the elevator and return to the exit of the TSA, past the android sentries, to the Global Transporter. Once more insert your ID card, and return to Caldoria (5).
As you saw early in the beginning of the game, the man who went to the rooftop was none other than Sinclair himself. Stand up, go to the elevator and select R. The door is locked so use the Card Bomb from Mars in the slot (10). You have 12 seconds to activate the Shield Biochip (5) and wait for it to explode or it will kill you.
Go outside and ignore Sinclair's paranoid warnings. AI warns you that there is an armed thermonuclear bomb nearby. You have 3 minutes to stop Sinclair before he kills the alien ambassador. You can't approach him from the observation deck. If you approach him, you have 15 seconds to leave or he will shoot you, so you must go around him and shoot him from behind the trees with the Stun Gun from WSC. Turn to W to walk around the western edge of the rooftop. Turn to the right where you should now see Sinclair, and you automatically telezoom to see him sniping. If you wait too long, he will kill the alien and the game will end. Use the Stun Gun by drag and dropping its icon on him, in the zoom window. He falls unconscious (10) but you now have to take care of the bomb.
Approach him and you will automatically operate the device and its "fusion detonator control matrix". It is a series of 6 dot to dot puzzles where you must trace the shapes in one "stroke" without crossing a conduit more than once. You have 10 minutes to solve all six or you will be killed. The puzzle is automatically solved on the easy level.
These are the possible solutions:
The bomb is diffused (10). Baldwin contacts you to inform you about the investigation concerning Sinclair, only to see that you have already incapacitated him. You receive congratulations from Baldwin and Michelle. Humanity is safe to enter its new era