Instructions
Run down the hall as soon as the cut-scene involving Harry Flynn ends. The main hall gate will close shut, so you won't be able to exit that way.
Turn right and run down the stairwell. There are no laser sights in the stairwell, so you can take your time in this area.
Climb up the window and jump over the side.
Immediately head to the manhole (it is the same manhole that you enter the museum courtyard from in the beginning of chapter two). Press the triangle button to open the manhole cover and automatically climb down the ladder.
Run across to the other side of the sewer. Soldiers with laser scopes will follow Nathan into the sewers, so you'll need to run quickly to avoid being shot.
Turn left and run down the sewer to the end.
Turn right into the last room and head to the ladder leading upward.
Press the triangle button to climb the ladder. The sequence will now end.