System Shock 2 Marathon Comparison Episode 2
Posted By: Lion O CyborgDate: 6/9/23 11:55 a.m.

System Shock Marathon Comparison & talkthrough Season 2: System Shock 2

Episode 2: Counterattack

Act 1: Fire! Fire! Fire! Fire! Fire! – Engineering: Coolant tubes

Welcome back to the System Shock 2 Marathon Comparison. In the first update, we learned about the game, did our training, created our character and explored the second deck of the Von Braun for the code that would let us into the first deck. That is where we are now. The maintenance access shaft leads down to someone’s bedroom a fair distance from the elevator, possibly that of an engineer stationed to work on the coolant tubes. There’s debris & someone’s hand on the floor and a log in the desk. It’s from Curtez: he found 2 rad hypos and plans to find a way past a turret but he’s found and killed by a hybrid or so it seems. Polito says she’s getting abnormal readings from this deck.

Xerxes warns people to stay out of the coolant tubes due to the radiation and threatens them with death if they don’t, not that the hybrids here actually listen to him. Maybe he just means uninfected crew members like us. Polito finds that I can’t get through the door to the engine core and I must purge the radiation from the tubes. She can’t help me as Xerxes is locking her out the primary data loop: he’s working for the Many now.

As I explore, Polito radios again:

“You must move faster. Your mind cannot conceive of the stakes we are dealing with. Keep your eyes open for utility storage 4. I’ve laid in some supplies there, the passcode is 59004. I must get to deck…”


“The Many demands the termination of this exchange. We regret any inconvenience.”


A different storage room is open and has some supplies in it including cyber modules. A few bodies in the coolant tubes have modules too. There’s also a log on the floor from Sanger. She says she can’t get in contact with any Rickenbacker soldiers to see what’s going on. Utility storage 5 is here too but we can’t get in yet. It serves as the chemical storeroom as well as holding a mission critical item we need later. Another log from Delacroix around a few corners has her complain to Korenchkin about him not letting people see what’s on Tau Ceti f and that he & Diego have closed off deck 3. Another log of hers outside utility storage 4 has her threaten to sic Bronson on him and Diego if they don’t explain themselves regarding deck 3.

Inside the storage room, I find nanites, hypos and a hazard suit. The suit looks like only the top half of one. Beyond the coolant tubes it’s pretty useless especially if you have the radiation and toxin PSI shields.

“Now listen carefully: the xenomorphs who’ve hijacked this ship are presumably from the surface of Tau Ceti V. They’ve been able to infect a number of crewmembers through an extremely invasive parasitical technique. They’ve also demonstrated the ability to control the actions of others through some form of limited telepathy. Find the research soft, understand them, then kill them.”

I’m not sure if it’s unlocked at this point or at the start of the main game but it’s worth saying that we can now learn exotic weapons skills. I won’t be using them except maybe level 1 as they’re very situational and you need high research skill to even use the two stronger exotic weapons. They also more or less become useless at the end of the game. As I reach the elevator on this deck, the voices from before come back.

“We do not know death, only change. We cannot kill each other without killing ourselves. Is your vision so small that you cannot see the value of our way?”

The middle bit with the pumps has cyber modules and nanites as well as a security computer guarded by a monkey. The pattern buffer for this section of Engineering is here to the left of the lift. Hacking then buying some med & PSI hypos from the vending machine, I find another log from Curtiz.

The strategy guide for this game combines this log text with the end log text of his first one in the bedroom where we started. I never noticed that misprint until now. Up the ramps nearby is Xerxes core on this level. Xerxes’s core serves as a sort of hub for the ship much like the central hub on Space Colony Citadel did in the last game though there is no easy access to each section from it unlike System Shock 1 and as seen here, the placement of his core is inconsistent with each level. As I approach and destroy the camera, Xerxes announces there will be a ship-wide census the next day and for all to report to either the Recreation or Command deck for that time.

The long hallway of bulkheads here leads to the cargo bay section. There’s a small lift on the left leading to a service corridor on the bottom of the ship connecting this hallway to the area near the engine core but it doesn’t work just now. Gravity elevators nearby connect to the engineering control room but the door is keypad locked. Sanger left an audio log by her broken shotgun saying she’s changed the door code to lock hybrids inside. She says she’s is going to hide in cargo bay 2 and to find her there.

Laser turrets are incredibly annoying as they’re hard to dodge and just as difficult to destroy as all other turrets and robots. For obvious reasons they don’t return in Bioshock but they do have an equivalent in the form of flamethrower turrets.

I recommend hacking security to disable them and them destroy them while they’re down. If you have hacking skill 4 you can hack them but I don’t so it’s worth just blowing them up. Without armour piercing rounds or energy weapons, smack them with the wrench while they’re disabled until they’re at low health, then it’s any ranged shot you want. The security station here contains nanites, cyber modules, some upgrade units, a log and some weird pulsing red organ sitting on a surgical unit. I take it and begin researching it. I then install the surgical unit activation key here then backtrack to level 2 using the hazard suit in the coolant tubes for some osmium to give the organ a nice seasoning.


Protocol droids have been reprogrammed by Xerxes and the Many to seek out threats and explode in their faces. The droids themselves are actually trying to be helpful and carrying out their original programming but they’ve been effectively enslaved and forced into suicide bomber roles. We start seeing a lot of them in the cargo bays. A log I missed from Bronson says the turrets have started going off against the crew and they can’t take them offline. She’s recalled the turrets to storage but can’t get in touch with the team sent out to do the recall. Chances are they got shot before they had a chance to dismantle the turrets.

Returning to the turret room I take the bulkhead to the cargo bay section.

Act 2: Gruesome Twoson – Engineering: Cargo Bays

No sooner do I enter this section next to a sparking metal machine do I receive a psychic vision projected to me by the owner of those voices I’ve been hearing, but not before the game crashes on the loading screen.

What…is that?

“We? We are a monument to all your sins. Do you not trust the feelings of the flesh? Our biology yearns to join with yours. We welcome you to our mass.”

“But you puzzle us. Why do you serve our mother?”

“How can you choose cold metal over the splendour of flesh? But you fear us: we hear your thoughts, and they rage for your brothers you believe dead.”

“But they are not. They sing in our symphony of life.”

“We offer another chance to join us. If you choose to lie down with the machine, we will rend you apart. And put you separate from the joy of the mass.”

That ladies and germs is the Many, specifically its main body. The wormy cage thing & bony hill in the middle of this fleshy chamber is their brain. Predating Halo 1 by 2 years and Halo 2 by 5, the Many is a cross between the Xenomorphs from Alien and a more polite, misunderstood version of the Flood, the body & brain being the Gravemind.

Unlike the Gravemind, the Many are all a collective of species who’ve become annelid creatures and no matter what form the individuals in the collective take, all work together and treat each other equally, the only form of inequality being if they need more biomass for larger creatures. Some crew members have joined them willingly and others haven’t. Others still…well, we’ll see what happened to them much later.

The Many genuinely want to make everyone feel happy and part of something good and joyous, but their morality is very different to ours: they can’t understand most people want their unique individuality and that the mutations the hybrids go through is often very painful and disfigures them. They don’t seem willing to listen to reason and we later find out we have no choice in killing them anyway so we can’t take them up on their offer.

The Flood on the other hand want any of their creations from their time as the Precursors feel suffering and dialog in the Forerunner Saga books implies they consider themselves the ultimate test for sentient life vying for control of the Mantle, like a trial by fire or something.

The sparks from hoses on the machine in this area can harm you so don’t get too close to them. On the floor by some crates of cigarettes and alcohol is a log from Rebecca Siddons to Tommy.

Annelid Healing Gland

Summary: This tissue can be used to systemically heal damage.

Analysis: The gland secretes a prolific mix of hormones and stimulatory enzymes, and a quickly dividing layer of cells spawns off multi-purpose circulatory cells. These cells seek out sites of tissue damage and graft themselves in, taking on the characteristics of the local host tissue in moments.

Recommendation: The shared tissue compatibilities between human and annelid tissue allow this gland to be used for healing, though not as fully as it would in an annelid host. Once removed from the host’s body, it can only be used once.

In short, we can eat those organs for health. Remember those eggs we saw in the vision? We can find them inside such eggs and we’ll be seeing a lot of those starting on the next level. I need to go to cargo bay 1 first as the door to cargo bay 2 is locked with a keycard.


“This is Xerxes. Can you not feel the glory of the flesh? Do you not yearn to be free of the tyranny of the individual?”


No. Homogenous countries with little to no diversity or the latter being looked down on and no creative freedom are a bad thing among human races alone including where I intend to live and work. I don’t need the same thing with aliens or mutants either!

A maintenance bot is lurking around here and there’s cases containing protocol droids. Don’t damage them or they will open, freeing the robot inside. Some break open on their own in the cargo bays which gets annoying.

PSI tier 2’s PSI flame shield helps reduce or negate the damage, but I don’t have it yet. There’s turrets nearby too. I hate the cargo bays: they’re repetitive multi-storey rooms full of crates with loot in them guarded by monkeys, protocol droids and maintenance bots. The first doesn’t have much of interest apart from a droid ambush when I get some nanites. I head to command control in a cargo hanger. It’s guarded by a laser turret but some explosive & radioactive barrels as well as some cryokinesis blasts deal with it as well as a leadhead hybrid near a recharger and a monkey on the nearby shelves.

A more believable drydock than the one in the map Smells Like Napalm, Tastes like Chicken in Marathon 1. The crates up there contain smokes, liquor and the odd packet of crisps or orange juice. A thuggish hybrid down a small hatch guards some ammo. The lower crates also have a log from Tommy warning Rebecca to stay put while he looks for her. A gravity lift leads up to a normal lift connected to command control.

Is that me? This ghost uses the same model. I’ve always wondered that, but later information seems to contradict it. Then again, given who is saying it at the time, it could be either.

A hybrid just rolled that head down here like someone skipping stones. Being careful to destroy the camera without being seen, I activate the pattern buffer which I why I came here: I need it. On the computer banks is a log from Diego.

Poor guy. He wanted so hard to not be like his father, though it isn’t entirely his fault: he just rushed out after Korenchkin before finding the Many. The second part of cargo bay 1 has some modules on the top floor. It connects to a similar hub area to the start of the bay with a log from the OSA guy Malone in a desk. Another log from him on a corpse (it can’t be Malone himself as the body appears to be female though it’s dark in here so I can’t tell) predates it.

"Malone Re: Psonic chimps!

“A laboratory worker from MedSci called me down to the vivisection room yesterday. He felt the lab monkeys were exhibiting uncommon intelligence. I sat with one for four hours and tried to probe it with a PSI amp on a beta 4 cycle. It failed to respond. I of course assumed because it was, naturally, incapable of reacting to the sophisticated beta 4 cycle. But then I realised it was blocking the probe intentionally! As soon as I raised the PSI amp to attack it, the creature lashed out with its arms and projected a cryokinetic field towards me, paralysing my arm. I immediately psi-dampened the monkey and then stunned it with an electric prod.”

Malone Re: Further Experiments

“Taking precautions, I proceeded with further experiments. Since we’ve reached Tau Ceti, the creatures have gotten smarter and somehow gained limited PSI abilities. I probed another subject with a beta 5 cycle and sensed many things, but mostly an incredible empathy. The chimps have become acutely aware of their own history; of the vivisections and experiments that have been performed on them while onboard the Von Braun. They have anger, and they are ready to express it. Clearly they are both a fascinating scientific resource and an incredible security risk. My recommendation: either freeze them in cryo storage for the remainder of the mission, or liquidate them immediately. Who knows what other abilities they’ll acquire?”

The monkeys must have become aware of that threat as they are still around and attacking any humans they see. The second part of cargo bay 1 has some modules near a sparking junction box on the top floor and I crush a monkey under the elevator as I go back down. The other half of cargo bay 1 on the other side of the entrance has more modules and protocol droid ambushes. I disabled security so the turret up top can’t attack me. The cargo bay 2 card is on a body on the bottom floor.

The first part of cargo bay 2 has a broken vending machine and I can’t repair it. One of the elevators here is broken too, being taken offline for repairs.

I think it’s possible to get those nanites without telekinesis but it’s very hard. There’s some more cyber modules up top as well as more nanites on the broken elevator. Carefully tiptoe onto the lift and jump off to safety as soon as you actually touch it because it falls when you do. Luckily, you can get the nanites by triggering the cargo elevator to fall and simply going back down, or use telekinesis again.

Dying to a protocol droid in the 2nd half of the cargo bay in order to make its explosion damage a hybrid, I end up being chased by one back to cargo bay 2. Besides their regular dialog, protocol droids make glitchy, crazy sounds that remind me of the malfunctioning Mr Friend robot clown dolls in an episode of Rugrats. Just watch that episode after listening to the droid dialog and you’ll see what I mean. Speaking of robots, the left cargo lift in this part of cargo bay 2 is broken except this time attempting to use it summons a maintenance bot! Try to avoid the button if you can and use the other lift. There’s already a bot here so I end up having to fight 2 and there’s a laser turret for good measure. Another bot waits in the next part of the cargo bay near Sanger’s body. There’s also logs from Diego and Delacroix. There’s modules here too on the second floor.

There’s a couple of logs I forgot I picked up from Bronson and Martin, the latter about coming to find Sanger for the engineering control code and the former about discovering how to hack the turrets.

She wasn’t safe in here: the robot found her.

Act 3: Never Burn Money – Engineering: Engine Core

Entering engineering control, Polito finds Xerxes is 1 step ahead of us and used an override on the computer. Luckily, Delacroix left a log: in the chemical storeroom we couldn’t enter earlier is a hardware override circuit board 45m/dEx. Install that into the systems monitoring unit in command control and it enables a backdoor into the computer.

Look familiar? System Shock 1 had objectives like this too but it is basically the same as Marathon’s chips. I level up my agility and energy weapons skills by 1 point when installing the chip and learn PSI healing & PSI flame shield.

Recognise that texture from System Shock 1? In a room at the back I find a lightsabre/laser rapier like in the first game on a dead body. This is why I levelled up my energy weapons and agility: I want that. Unfortunately I need another point of energy weapons to be able to use it. Luckily, the cybernetic modules from the next objective as well as those hidden behind the starboard nacelle should help.

This is trippy. The other nacelle (starboard again) has a cache inside it and the modules behind it. Delacroix has some interesting information to share.

Upstairs past some worms on the floor is another log from Sanger. Delacroix was arguing with Korenchkin after he became a hybrid. He blows her off, saying she doesn’t understand the glory of the Many. I hit the big monitor button and turn on the elevator.

“Good work. The engine core is back online. Now get to the elevator and come see me on deck 4. While you were doing that, I’ve discovered some annelid artefacts onboard the ship. I think you may be able to use them to your advantage. I’ve uploaded the information to the ship’s weapons upgrade units. They’ll be able to convey the information to your cybernetic rig. What are you waiting for? Get to the elevator now.”

Patience, Doctor. This is a bit different to Marathon in that alien weapons could be used but we couldn’t reload them. Now we can research how to use the weapons and learning further via exotic weapons skills allows it to not only wield but reload them too. For that we need those worm piles though for me it’s much more efficient to recycle worm beakers and eat the worm piles for lunch.

Taking the elevator to the underpass corridor, I find more modules and stuff in security crates and on bodies. At the end past a turret and some leadhead hybrids is a new enemy.

The cyborg midwife. Made to take care of the Many’s eggs while being protected from toxins inside them. They’re super annoying to fight: they have laser pistols, take less damage from regular ammo and fire is weak against them. Luckily, dying to this one let me level up my energy weapons enough to slice it apart with the laser rapier. We’ll be seeing a lot more of those girls on deck 3. We also have the chance to see a lone Many worm wandering the coolant tubes but it didn’t spawn this time.

Laser Rapier

A brutally effective melee weapon, the Laser Rapier requires an Agility of 3 and an Energy Weapons skill of 4 in order to use. Far more effective than the prototype model first developed on Citadel Station in 2072, the Mark IV laser rapier is a much more reliable piece of technology. The unit works by projecting a porous field of reflective material in a shaft shaped region around the base of the rapier. When the material is bent (as when the rapier strikes a target), the intense refracted light inside is released locally, causing intense burns to the target. “That’s right, just like the one the Hacker used on Citadel Station! We’re the only one in town who’s got ‘em! Only 40 nanites!” – Street vendor selling laser rapier replicas in New Detroit.

The lightsabre isn’t as effective as the original one as it’s supposed to make way for the first exotic weapon we can find. I might take that one too but I want to use this one. It sort of returns yet again in Deus Ex in the form of the Dragon’s Tooth sword, which isn’t a lightsabre but a nanobot based version of Durandal the sword. I still don’t have an auto repair kit to fix the broken laser pistol I found in cargo bay 2 so I’ll need the laser rapier for robots and cyborgs. I think it’s time to throw away that wrench.

That can’t be good! I need to go to level 3 first. Polito can probably tell me what’s going on. Next episode: we visit the Hydroponics deck in order to unblock the elevator shaft.

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