The final O/S Upgrade waits for you in this room, guarded by a Rumbler. Use your Rickebacker Access Card and open the door ahead. When they're gone, SHODAN will likely continue to pester you about your hesitation some more. Use caution going forward, as several unavoidable Annelid Swarms will attack as you step out - run around a little bit to keep them away from you. Her suggestion is to take an escape pod at the back of the bridge and plunge yourself into the Many, in order to take the fight directly to them.
It seems that the Many have literally engulfed the exterior of the Rickenbacker and Von Braun, meaning it's now impossible to separate the two ships. Hold up as you exit the Elevator from Pod 2, as SHODAN will contact you about three times in succession.