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1 - Bridge Entrance
Hold up as you exit the Elevator from Pod 2
, as SHODAN will contact you about three times in succession. 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. 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. Sounds... er, reasonable.
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. When they're gone, SHODAN will likely continue to pester you about your hesitation some more. Use your Rickebacker Access Card and open the door ahead.
2 - O/S Upgrade Unit & Office
The final O/S Upgrade waits for you in this room, guarded by a Rumbler. Dispose of it, keeping out of range of the Security Camera around the corner to the left, then make your final O/S Upgrade
choice - at this point it doesn't matter too much, but anything that increases your damage or efficiency is good to have.
Take a right through the door and check inside the small office, fighting off an Annelid Arachnid and another Swarm Pod. The corpse inside contains a bunch of Anti-Personnel Shells and a Maintenance Tool. Backtrack, ignoring the ladder to the Escape Pod for now, and sneak into the next room.
3 - Computer Core & Upgrade Units
This large chamber has several more Rumblers
in it, about three in total, and three Turrents, one Missile near the door and two Lasers at the end of the room. They're not making it easy for you! Use whatever means you have to kill them off, then go to down on the full suite of Upgrade Units available. This will be your last time to upgrade before the endgame, so make those Cyber Modules count.
At the lower end of the room you'll find a Security Control Station, if you want to use it, but not much else save for the loot on the destroyed Laser Turrets. Climb back to the top, near the Bridge doors, but continue instead to the next room.
4 - Computer Consoles & Replicator
In the room with all the computer consoles, you'll find 24 Nanites sitting under one of the desks, and just nearby, there's some shelves with several Disruption Grenades and two Small Beakers. The Replicator nearby is broken, but can be repaired, and sells EMP Grenades, Psi Hypos, Maintenance Tools, and Juice, the latter of which changes to Prisms on a successful hacking attempt.
Proceed into the door at the end of the hall to reach Diego's Quarters - you'll need the Diego's Quarters Access Card from Diego's corpse back in Rickenbacker Pod 2.
5 - Diego's Quarters
You'll be attacked by a large number of Annelid Grubs as you come in. Dispatch them, and you'll notice a large... Annelid... thing on the floor. Pick it up to receive the Annelid Launcher
(requires some researching), the ultimate in Exotic weaponry. SHODAN will even give you 20 Cyber Modules just for doing so. Depending on how you specialise it may not be worth using, but it's certainly powerful, and it fires homing shots to boot.
Beyond that, there's a few piles of Worms on the floor to fuel the Launcher's ammunition needs, and 24 Nanites on the bed's pillow. Time for a quick stop at the Bridge.
6 - Bridge
Finally, the Rickenbacker's Bridge... okay, so it doesn't look too much more impressive than the rest of it. Unfortunately, the loot available is a little anti-climcatic too, as you'll find a paltry 24 Nanites underneath a desk and little else. You will, however, notice the Many pressing up against the ship's windows, and there are a few control panels with readouts detailing the infestation.
Alright, that's enough of that. Time to find that Escape Pod.
7 - Escape Pod
Backtrack to the ladder you passed by before entering the Computer Core, stopping to grab yet another pack of 24 Nanites from the floor, behind one of the crates. At the bottom of the ladder, you'll find a bunch of Anti-Personnel Bullets on the corpse, along with a Maintenance Tool. Destroy the Annelid Arachnids that come down the hall towards you, as well as the Swarm Pod, then continue down the corridor to find yourself in the escape pod.
This is it, the last moment before you're locked into the endgame. After pressing the button to launch the Escape Pod, you will not be able to return
to either the Rickenbacker or the Von Braun. If you have any more doors you want to hack, items you want to pick up, objects you want to research, upgrades you want to perform, ammo you want to buy... now is your last chance. You can even travel all the way back to MedSci if you really want to.
When you're ready to take the fight to the Many, press the button on the control panel to launch the escape pod... and crash into the Body of the Many