While you are in the transporter, you have 5 minutes to exit or it's a game over. After you exit the transporter, you are in a long corridor. Walk it and click on the door with the TSA logo to open the door, and see Michelle scolding you before leaving. You enter the Annex (2).
Once inside, you are in the Hall of Suspects with six busts of important personalities of the game's universe. Feel free to check each one of them (2x6) and listen to their quotations. Continue to the N and pass the sentry robots. The Command Center is to the W and the Ready Room is to the E.
Go to the W and follow the corridor, turn around and enter the door to the Command Center. Walk around the structure either left or right, then turn and walk inside to sit. You get a message from Baldwin who scolds you once more for being late. You are grounded and obliged to re-educate yourself to TSA procedures, and a good oportunity to learn more backstory. You are redirected to a monitor where you can review TSA Background (4), TSA Theory (4) and TSA Procedure (4). When you finish (or just skip) the 3 videos, an alarm sounds and Baldwin orders you to go to the Ready Room. While the alarm sounds, you have 10 minutes to use the Pegasus Device or the Temporal Ripple catches up with you and alters your universe and game over.
Turn around, go forward to exit the structure and walk around to the door. Traverse the corridor to the very end where the Read Room door is and enter it. The structure to the right reads Mission Biochips and will give you the Mapping and Pegasus Buichips which you can take to your inventory (5). The case to the left opens the same way and gives the Historical Log Access Key (5). Once you have both items, walk inside the tube in the center to have a BioSuit encapsulated on your body (5).
The turbolift brings you down. Walk forward to the circular rail until you face W and turn around to the Pegasus entrance. Go inside and receive the messages from Baldwin and the AI. Once all is ready, click on the JUMP to travel to Prehistoric (5).