Credit to the walkthrough guys for the description:
Start the chapter off by choosing whether or not to let Shade come with you. I always just say yes because he's a crazy, lonely man. Then, just follow along the vent until you can place the EMP. Now, you can watch what Rhys really did at the end of his story. Eventually, you will have to activate the EMP. Shit will go down and you will meet a human dubstep machine and an awesome number. Push down the fan and choose whether or not to shoot at August. Shooting is a complete waste, so save it.
On the caravan, you will have to mash
to escape. Now, tell the stranger 'what happened'. Definitely choose to calmly discuss an alliance.
Start going through the dialogue and eventually just mention that you have Nakayama's ID drive. You'll now install it into your head... you end up with more than just his credentials.
Here is a video of the chapter:
Credit to DanTheMan.