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1 - Escape Pod Crash Site
You'll find yourself in the wreck of the escape pod from the Rickenbacker, driven deep into the Body of the Many. As you turn to leave into the mass of flesh, SHODAN will tell you that she will not be able to keep contact with you... finally, a little peace and quiet. Your goal in the Body of the Many, for now, is to destroy two Nerve Clusters in order to open a way forward, though you technically won't learn of that until you reach the area at (5).
The way forward here is very straightforward... simply follow the fleshy, gooey path ahead. You'll eventually come to a tunnel, and a bend, with an Audio Log on the floor by some crewman who was dragged inside here. But how to get in? The wall in front of you is actually a door - shoot it or smash it to gain entry, though you'll come under attack by an Annelid Arachnid as you open it.
2 - Juncture
Beyond the door, the Many will speak to you and once again tell you to surrender. Pssh, yeah right. The corpse ahead has some Heavy Combat Armor and a Psi Hypo on it, and there's yet another Crystal Shard on the... er, ground nearby. For now, head just past the corpse, and take a right. You'll likely fight a Rumbler as you explore the area, so dispose of it if need be.
3 - Rickenbacker Wreckage & Replicator
You'll be faced with part of the Rickenbacker as you approach, consumed by the Many. Jumping through the windows will cause some Swarm Pods to hatch, so back off for a while and return shortly. Inside, you'll find a Grub Pod to destroy, a Replicator, some chemicals, a bit of loot, and a bunch of chemicals you'll need to research some of your recent finds: two Molybdenum (Mo), two Technetium (Tc), and one Tellurium (Te).
The Replicator is selling Juice, Anti-Toxin Hypos, Psi Hypos, and Medical Kits, and can be hacked for Proximity Grenades. The locked secure crate has a stash of 53 Nanites and some Anti-Radiation and Anti-Toxin Hypos, while the corpses have 10 Cyber Modules, 71 Nanites, an Anti-Radiation Hypo, and some Prisms, though as you loot them, Annelid Grubs and Swarms will attack you.
When you're finished tending to your shopping needs, hop out through the window and return to the Juncture (2), then turn around and go down the door you passed by earlier, down the steep slope.
4 - Nerve Cluster 1 & Psi Reaver
Smash through the membrane at the bottom of the slope and you'll find yourself in a pool of water, with a Psi Reaver to keep you company. Dispose of it and its Brain Structure (underwater near the floating corpse), then surface and you'll notice a large organ on the ceiling to spot the first Nerve Cluster you need to destroy, so go ahead and get to business. A few treasures await you in here as well: the body bag has 10 Cyber Modules inside, the corpse holds Anti-Radiation and Anti-Toxin Hypos, and there's some Proximity Grenades at the bottom of the pool.
Nerve Cluster thoroughly destroyed, it's time to leave this murky, watery hole. Find the exit guarded by a membrane and take the path out. It winds quite a bit, but simply keep going straight and you'll soon find yourself near the Juncture earlier; if you didn't kill it already, there's a Rumber around here waiting for you. When it's safe, proceed through the tube-looking orifice in the wall, marked by some dripping, green liquid.
5 - Juncture 2 & Audio Logs
Grab the Audio Log from the floor as you pass through the orifice-door, and continue a short ways to find yourself in a large chamber. The small organ on the floor releases some sort of white particle that pushes you back, but it can be easily avoided and won't hurt you. Grab another Audio Log from the floor in this room, and you'll also find a Viral Proliferator and corpse with a Psi Hypo and some Worm Clusters.
The Audio Log provides some information on how to proceed - by destroying the two Nerve Clusters. If you've followed this guide, you'll likely have already destroyed the first one, but if not, you'll need to backtrack to the area at (4). Otherwise, take the orifice-tunnel to the left to reach another piece of the Rickenbacker.
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 - Rickenbacker Wreckage 2
Yet more of the Rickenbacker awaits you in here. Again, it's a dead end, but you'll discover a Maintenance Tool on the floor, Version 3 Research Software and a Psi Hypo on the corpse, and 63 Nanites in the secure crate. Additionally, there's a few more chemicals on the floor: Barium (Ba), Tellurium (Te) and Cesium (Cs).
When you're finished exploring the ruins, make your way back to the previous area, and take the path forwards, then take a left at the first bend.
7 - Irradiated Pool
Hope you still have that Hazard Suit! If not, you'll have a use for all those Anti-Radiation Hypos you've been finding around. Fight off the Annelid Arachnid that comes up the tunnel towards you, and dive in. Immediately upon swimming in, you'll find a corpse with some Annelid Armor, a WormHeart Implant, and some Anti-Personnel Bullets. Swim all the way down and grab the Medical Kit, then search the desk for an Anti-Toxin Hypo and an Auto-Repair Unit, then proceed through the next orifice.
The path will split into two, and the Many will speak to you again. Left or right, you'll end up in the same place, so pick your poison. In the next chamber, you'll find a corpse with a Crystal Shard, with another one floating near, while a second corpse has a WormHeart Implant and a Medical Kit close by. Follow the "blowhole" up to the very top, smash through a membrane and grab an Anti-Toxin Hypo, 73 Nanites and a few Disruption GRenades from the corpse, then swim back down and leave through the final orifice (the one near the Crystal Shard).
8 - Nerve Cluster 2
Take the path along and you'll come into another large chamber with some heart-like organs inside. Follow the irradiated waste barrels and you'll eventually emerge next to a couple of corpses and the second Nerve Cluster. Take the 10 Cyber Modules, Worm Clusters and Viral Proliferator from the bodies, then shoot the Nerve Cluster. When you're through, turn around and backtrack out to the main passage you came in from.
9 - Watery Tunnels
Despite the title, there's no swimming just yet. Break through the membrane and you'll find yourself in a tunnel area with a patrolling Rumbler and an Annelid Arachnid. Deal with them as you see fit, then take the path left, towards the small shelter, and loot the corpse for 57 Nanites and a Psi Booster. Continue onwards and you'll find another corpse with 6 Cyber Modules and some Standard Bullets, and a Cyborg Midwife. Dispose of the murderous nanny and enter the passage on the left.
10 - Rickenbacker Wreckage 3, Upgrade Units & Chemical Storeroom
You'll likely come under attack by some Annelid Swarms from the Swarm Pods ahead, so destroy them and run past to find yourself in more ruins of the Rickenbacker. This is the remains of a Chemical Storeroom, it seems, so grab whatever you need from the many, many vials. There's also a much-needed Recharging Station inside. The few corpses in the vicinity hold some Anti-Personnel Bullets, a Medical Kit, and more Anti-Radiation and Anti-Toxin Hypos.
The lounge up ahead has a full complement of Upgrade Units for some last-minute improvements, and the Replicator sells Prisms, Anti-Personnel Shells, Anti-Toxin Hypos and Chips, which can be replaced with Anti-Personnel Bullets. The next room has a bunch of Annelids inside, Swarms and Grubs alike, so end their parasitic existence before turning your attention to the corpse (Anti-Toxin Hypo and 50 Nanites) and secure crate (67 Nanites and some Prisms). This is one of your last chances to really stock up on upgrades, so your best bet is to buy as much anti-personnel ammo as you can - those Nanites are just going to be wasted otherwise.
Your spending and upgrade spree complete, it's time to move on. Backtrack to the tunnel where you found the Cyborg Midwife and you'll spot a side passage you can crawl inside, marked by some blue nerves.
11 - Sphincter & Audio Log
Right here you'll find the sphincter mentioned in the Audio Logs you'll have picked up on your travels through the Body of the Many. If it's closed, you'll need to hunt down the two Nerve Clusters around the area, as described above. If it's open, well, good on you.
The Audio Log on the floor contains a grim portent of the area ahead, while the corpse has Psi and Medical Hypos on it. Just ahead, you'll run into a Cyborg Midwife and Annelid Arachnid to fight off, so make your way past them and enter into the next room.
11 - "Mouth" Room
The next area is rather interesting - massive teeth move up and down on the other side, crushing anything caught between them. Before checking them out, examine the corpse in the pool of water for 67 Nanites, and the makeshift shelter for some Prisms, a Psi Booster, some Fragmentation Grenades, and a Maintenance Tool. If you have Psi Pull, you might be able to snag the Anti-Personnel Bullets and 17 Nanites from the small structure above, but I found it exceedingly difficult to do so, and not really worth the price in Psi Points.
Approaching the teeth, you'll stumble over another Audio Log to listen to, and a Cyborg Midwife will attack. Destroy the evil machine, then grab the 5 Cyber Modules and Standard Bullets from the corpse. Defeat the Annelid Arachnid lurking about, then head down the passage to the next room.
11 - Jumping Puzzle & Nerve Cluster
Everyone likes jumping puzzles! No, not really? Well, this one isn't too bad. Before starting, explore the bottom area to find a small passage containing a corpse with 10 Cyber Modules and 53 Nanites. Back in the main room, you'll need to jump from tooth to tooth, clambering up the blue nerve-ladders on the walls to the very top, where you'll find a Nerve Cluster. Climb back down and you'll find the sphincter-door has opened, so jump to it and head on through. It's not very challenging, but just be sure you don't get crushed by the teeth.
In the next corridor, you'll be assaulted by another Rumbler, so put the big guy down and then search the corpse on the floor for Version 3 Modify Software and a Maintenance Tool. Continue forwards, avoiding the particle-jet-things on the floor.
12 - Hub Chamber & Makeshift Shelter
Another room, another Rumber, though this one is backed up by a couple of Annelid Arachnids and a Cyborg Midwife. You'll find another Audio Log in the desk describing the role of humans in the Many's feeding, while there's a Crystal Shard, Psi Hypo and Disruption Grenades under the makeshift shelter.
Right now you have a bit of leeway on where to explore. If you want to find all the loot you can, keep reading, otherwise, take the forward passage out and skip to section (15).
13 - Rickenbacker Wreckage 4 & Cyber Modules
Turn left and you'll find yourself aboard the remains of the Rickenbacker; destroy the four Swarm and Grub Pods, then loot the bodies for Incendiary Grenades, Prisms, Anti-Personnel Bullets, another Annelid Worm Launcher and some more Prisms. The garbage can has 6 Cyber Modules and 47 Nanites, while one of the storage crates has a cache of Disruption Grenades. Last, search the desk for an Audio Log and Large Beaker.
14 - Womb Area
Follow the exit past the shelter to reach this second optional area. The corridor once again branches off, and you'll be attacked by a few Annelid Arachnids on both sides. To the right, you'll find some Swarm Pods and corpses with 10 Cyber Modules, Annelid Armor and a Maintenance Tool. To the left, it's yet another branch, with the left leading to another egg-containing room, with the corpse inside yielding Worm Clusters, a Psi Hypo and Anti-Toxin Hypo.
If you follow the path to the right, you'll enter into a large flooded area. Cut through the membrane and the Many will taunt you once more. Swim through the tunnels and you'll eventually come across a "womb" area, with two Cyborg Midwives and an Annelid Arachnid standing guard. Defeat all three and proceed until you reach a chamber with some corpses and four eggs scattered about. Destroy them from a distance, and you'll find 10 Cyber Modules, a Crystal Shard, an Anti-Toxin Hypo, and some Disruption Grenades on the corpses; there's also a Large Beaker on the floor. As you leave, there's one final room in another side passage, this one with three Annelid eggs. The corpses in here have Incendiary Grenades, Prisms, Annelid Armor, Worm Clusters, Disruption Grenades, and 57 Nanites.
With buckets of loot in hand, backtrack to the central room where you fought the Rumbler and his friends, then take the main passage out.
15 - Narrow Room & Audio Logs
Not sure what I'd call this room, but it's the one with the low ceiling immediately past the Hub Chamber (12). You'll know it by the supply crate on the left-hand side and shelter on the right. An Annelid Arachnid will attack as you enter, and you'll also spot a Rumbler on patrol in the corridor ahead. Defeat the two, then pick up two Audio Logs, one in the crate and the other near the shelter. Meanwhile, the corpse will offer up a Medical Kit and an Anti-Toxin Hypo.
Proceed forward when you're done into the next passage. At the end, there's a membrane blocking the way. Break through and you'll find a pool of water at the bottom... it's a long way down, so plug your nose, make sure you have everything you need from the previous areas, and take the plunge.
16 - "Stomach" Room
At the very bottom, you'll find three corpses, but nothing in the way of enemies. Snag the Anti-Personnel Bullets, Prisms, and Psi Hypo from the bodies, and yet another Crystal Shard if you really, really need one. Swim up to the top and climb up the ramp, where you'll encounter a Rumbler and a Psi Reaver. You won't be able to find the Psi Reaver's Brain Structure just yet, so content yourself with the Audio Log on the floor, the Large Beaker, and the Broken Pistol. Proceed into the next area.
The corpse on the floor here has some Fragmentation and Proximity Grenades on it, and there's a Rumbler just up ahead. Before you run forward, look up for a ledge near the ceiling; you can use one of those particle-jets to jump up to it, where you'll gain a decent vantage point, plus some Prisms and Anti-Personnel Bullets. Carefully hop down (you'll almost certainly take damage unless you land on the jet), and make your way forward.
Along the way you'll encounter more Rumblers and Psi Reavers to fight. Again, don't worry about the Brain Structures, just keep moving.
17 - "Brain" of the Many
The Many will speak to you as you near this room, where the final showdown with the Many will take place. This upcoming fight is extremely tough, so it's recommended you use a good deal of your supplies to heal up as best you can - but not all of it. You will also outright need to use a ranged weapon of some sort - your melee stuff, even the Crystal Shard, won't be enough. Step in, and you'll be face-to-face with the closest thing you could call to the "boss" behind the Annelid infestation.
In this large chamber, you'll find near-endless Rumblers and Psi Reavers, plus a couple of Annelid Arachnids and Cyborg Midwives. Be fast, and keep moving, as just getting into this room is difficult! Inside, you won't be able to damage the Brain directly, so instead run around the left and right sides of the chamber, destroying the Brain Structures (three on the left, two on the right). Next, your goal is to destroy the three floating stars that wrap around the Brain - just about any ranged weapons will do. When that's done, you'll be able to damage the Brain itself; it only takes a few shots.
If you're having trouble with the immense number of enemies in this room, especially on harder difficulties, the easiest way to cope is to use Psi Invisibility to bypass the enemies, though you'll still need to be visible to attack. Otherwise, heavy weapons like the Grenade Launcher, the Stasis Field Generator, and high-damage guns like the Assault Rifle will be your best hope.
The enemies won't actually stop attacking you after destroying the Brain, so there's only one thing you can do - climb up to the top of the leftover stem, and jump inside, following the long, winding tunnel on the current. The Many will tell you it is dying, and offer one final warning for you regarding SHODAN. With that said... just what does she want next? And where are you going?