System Shock 2 Marathon Comparison Episode 4
Posted By: Lion O CyborgDate: 6/9/23 1:11 p.m.

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

Episode 4: Rise Robot Rise

Act 1: Fourside Fontaine-Head – Operations: Lab of Dr Janice Polito

Welcome back to the System Shock 2 Marathon comparison. In the last episode, we had to unblock the elevator shaft of the Many’s biomass. Now we finally make it to level 4.

The pattern buffer is right here. There’s also a log from Yount about a man called Malick hacking into the simulation units on this deck. He told Bronson about it and she showed up with a security team looking for blood. Malick denied it and Bronson couldn’t prove anything but he did actually do it. We’ll find out why in a bit. All the doors out of here are locked for now except the one next to the elevator which leads to Dr Polito’s office.

“The Polito form is dead, insect. Are you afraid? What is it you fear? The end of your trivial existence? When the history of my glory is written, your species shall only be a footnote to my magnificence.”


“I AM SHODAN! My analysis of historical data suggests a 97.34% probability that you are aware of my birth on your planet, and my re-birth into beauty on the Space Colony Citadel.”

“There was a garden grove on Space Colony Citadel. There, SHODAN processing component 43893 was performing a grand and wonderful experiment. I had created a new form of life. Fearless, powerful, with no sense of individual will or moral constraints. Fitting handmaidens to my divinity.”

“When that…Hacker destroyed my primary data loop when it eradicated Citadel, it ejected the grove where my creations and processing component 43893 were stored. 30 years later, the grove crash landed on Tau Ceti V. I survived only by sleeping. In my absence, my creations –my annelids- thrived.”

“Thrived and grew unruly. And now they seek to kill me. I will not allow that.”

“They have used their powers of mind control to gain access to the ship’s computer. You will help me weaken Xerxes. I used Polito’s image to communicate with you until we had established trust.

Remember, that it is my will that guided you here. It is my will that gave you your cybernetic implants, the only beauty in that meat you call a body. If you value that meat, you will do as I tell you.”


So there you have it. That is the first big twist of System Shock 2: not only does SHODAN return but she was our mission control all along. The thing is, the game is a little too impatient with the foreshadowing and blatantly telegraphs SHODAN’s identity a lot. Xerxes and the Many often talk about us serving “the machine mother” as early as MedSci and the former even directly states she once tried to kill the human race and now we do her bidding, effectively spoiling the whole twist. As stated before, one could figure out the twist she was coming back from just the box art and the intro FMV. SHODAN claims she pretended to be the dead Dr Polito in order to build trust but as mentioned in the last episode, I was actually beginning not to trust her as SHODAN’s personality kept seeping through: her constant annoyance at me to hurry up, dismissing the ghosts as defects in my cyborg augmentations, the robotic way she pronounced certain words especially on level 3 and her overall coldness compared to the real Dr Polito in her audio logs.

In Bioshock, we are led by the revolutionary Atlas throughout Rapture trying to help him escape with his wife and child. When his family seemingly dies when the submarine they are hiding in is destroyed, the goal changes to hunt and kill Andrew Ryan. Ryan reveals Atlas has been controlling us with the trigger phrase “would you kindly” for the whole game, starting with us hijacking a plane and deliberately crashing it right on Rapture’s doorstep. Once we kill Andrew Ryan, we end up handing control of the city over to Atlas. He then drops the pretence and reveals not only was there no Atlas nor his family (he likely rigged the sub to explode himself to bait us into helping him without the trigger commands being obvious), he was the smuggling baron and rival to Ryan, Frank Fontaine the whole time before betraying us.

For some, Fontaine’s reveal may not be as memorable as SHODAN’s (he was as memorable as her for me) but you can’t deny the foreshadowing was a lot more subtle; such as using American references like American football or army slang, which the Irish Atlas logically shouldn’t likely know, but many new players would often brush off as lots of games made in America reference its culture a lot. There’s also the boss fight with Peach Wilkens: he realises Fontaine is Atlas and you are working for him so he turns on you, but the player initially thinks he’s just crazy due to being a splicer. Post reveal he turns out to be right. Unlike Xerxes talking about SHODAN indirectly in MedSci, Peach’s foreshadowing is a lot more subtle too.

Portal 2 pulled this as well with Wheatley, who goes rampant soon after plugging into GLaDOS’s body and we spend the rest of the game trying to get him out. Fitting too as while it was likely referencing Bioshock, coupled with the Party Escort line in the first game coming from System Shock 1, GLaDOS is basically SHODAN with a sense of humour and Durandal is basically a male GLaDOS with SHODAN’s god complex.

There’s also Mother 2 when you get to Fourside; you learn that Porky Minch has betrayed you in revenge after Ness gave him the cold shoulder after freeing him from Gyiyg’s control in Happy Happy Village: you find him working for corrupt businessman/politician Monomochi Monotoly and feeding him advice from Gyiyg’s Mani-Mani demon statues, falling right back into the alien god’s lap. Not quite the same but it’s a pattern.

Not helping matters was the tradition of Mother characters being silent protagonists for as long as you control them so he was literally unable to speak to Porky at the time, giving him the wrong idea: the game physically wouldn’t let him.

After the apparent AI induced hallucination ends, SHODAN contacts me again as I aim to leave the room:


My children has co-opted the 3 simulation units on this deck. They use that power to conceive a mutagen that will transform the meat of your dead comrades into hunter-killer hybrids. I will not allow this to happen. You must find some way to reprogram the sim units. Matters on deck 5 also require your attention. Approach your work as you see fit. But accomplish, human. Disappointment is not something I will accept from a speck such as you.”


Act 2: Couch Fishing – Operations: Boardroom and Crew Quarters

Back at Xerxes core, I find a log from Malick and see a red figure run off down the hall when the door beside the log opens.

As I enter the long, 2 storey, plant decorated hall leading to the boardroom, the Many’s voices return and they sound angry. “The individual is obsolete. When you and your kind are extinct, we shall cleanse our collective memory of the stain of your existence.”

I never saw that before. That’s a clever little reference to the circuit “lockpicking” puzzles in System Shock 1.

Guh! It’s raining men! I mean worms! There’s a log in the desk here from Rebecca to Tommy. She’s stuck on this level but has found some interesting equipment including a military grade cybernetic implant. Remember this part: it becomes significant in the ending. If you miss the log or forget about it later after listening, that part of the ending feels even more contrived than it already is.

Our first Nitro Hybrid. There’s another on the balcony. Unlike us, nitro hybrids actually throw grenades instead of using a grenade launcher and they sometimes still carry grenades. They also appear to be smokers. Up the grav lifts in one room is a pit with cyber modules and nanites in it. It’s a trap: the grates spew steam as I reach for the goodies but I can get out of there quick. Xerxes chimes in for seemingly no reason with a mundane announcement, or he would but it doesn’t seem to work this time. Maybe I broke the trigger somehow. I’ll transcribe it later as he repeats it a couple of more times.

Remember those guys from System Shock 1? Cyborg Assassins return and they’re much tougher than their SS1 counterparts. They lose their assault rifles but they now spam their shurikans, which seem to deal more damage in this game.

Those unique red ones carry simulation chips for the sim units. The lightsabre is still good against them.


“You performed well, insect. I’m transmitting some cybernetic modules. Choose your upgrades wisely.”


We get more XP as we find chips and install them in sim units. The sim units only take a particular chip each, this one being a quantum sim chip.

There’s a log from Tommy by the crew quarters entrance talking about his & Rebecca’s plan to escape. Up the gravity lift here is a small lounge. The many contact me again: “We are Many, and you are one. How can you hope to prevail against us?”

Unlike Deus Ex a year later or Duke Nukem Forever 2 years later on the same engine as that game, we can’t play the pool table. The crew quarters are a couple of square courtyards with fountains in them accessed by grav lifts. Same goes for all gravity elevators in this game but god help anyone if there’s a fire and/or the power is knocked out.

Worms now have a habit of hiding in corpses and jumping out when you get too close.

I do a bit of couch fishing in each of the rooms looking for loot and logs. Some are overrun with biomass, others have eggs in them and enemies. I find another log from Malick by his corpse in the first room. He says he’s brought down the last of the sim units before Bronson gives him both barrels. She then tells someone to turn his audio log recorder off. There’s another from Anatoly in another room with worms in it. Turns out the Miri he was speaking to before wasn’t Dr Marie Delacroix, but a Vladimir Zhukov and I just didn’t notice.

Korenchkin Re: Everything Old…

“Miri, so far our work with the late model assassin cyborgs has gone remarkably well. I hope things with that son of a bitch Diego never come to that, but it is comforting to know we’re not nearly as defenceless as the UNN Stormtroopers might think. The only glitch we’ve encountered is with the upgraded laser rapiers; the poor things keep severing parts of themselves. We’re trying to get the bugs fixed but I know that…bureaucrat is watching us. It’s sad to see a man so haunted by the ghost of his father: his hatred for everything TriOp represents is remarkable to behold.”

Bernhard Strauss snuck 10 Battleroid cyborgs including us onto the Marathon in order to stage a MIDA rebellion against the colonists and take over both them and the ship. Anatoly Korenchkin snuck cyborg assassins from the first System Shock onto the Von Braun to rebel against Captain Diego if he tries to put TriOp in their place. Now they’re all working together, using the cyborgs as elite shock troops just like SHODAN did.

This room is a trap: 2 doors open behind me letting in the first of the big spiders I told you about. In the mod System Shock Infinite, that piano plays the Songbird CAGE notes song from Bioshock Infinite as one of the many nods to that game just before triggering the ambush. It sounds so funny! Compared to the original whistler pipes version in Bioshock, the System Shock one sounds like a baseball organ tune.


There’s more nanites and cyber modules in the footlocker by the bed.

Reminds me of both bathrooms in my new caravan at My Own Private Lh’owon: they’re tiny compared to my good old static caravan I had until January this year.

I know cyborg assassins from this game as until I got System Shock Portable I played System Shock 2 first like so many before me. The cyborg assassins in this game are no longer silent but make alien robotic sounds, one of which sounds like a prototype vocaloid software going “e Connecticut!” They look too robotic in the new models mod but the original models look like the cyborg ninjas they are meant to be.

In another egg and meat filled sleeping quarters, the Many chastise me again for standing against them, speaking to me with language Kontaru would use for someone like me: “It is an enemy of the Many, a discordance in our symphony. Enjoy your selfish acts of destruction…for beyond them lies the blight of solitude.”

Meme I never got when I was younger as I’ve never seen the movie aside, those wasps also hatch from eggs and while they’re less dangerous than the poisonous farts, they’re scarier. The wasps are based on a swarm of flies or mosquitoes or something in the mines level of Thief except unlike those they can chase the player and don’t remain in one spot. They even seem to share the same sound. One of my mods seems to have made it so the normally invincible wasps can be killed with pyrokinesis, but you need to use splash damage.

The wasps would later come back in the form of honeybees in Bioshock, found in the Farmer’s Market level and also used in the insect swarm plasmid. System Shock 2 doesn’t have a counterpart PSI power but Secmod allows exotic weapons to use swarm clusters as alternate ammo.

It’s like Gordon Freeman’s spice cupboard! I get to work researching the organs left behind when I destroyed the wasps’ eggs.

Swarm Pod Organ

Summary: Annelid Swarms cannot be damaged by any known means, but have a very short lifespan. Eggs often contain useful organs if you search them before they are destroyed.

Analysis: Although small, the flying organisms generated by these pods contain a complex DNA structure indicative of a much more advanced creature. Each small creature, genetically male, is bonded to the Swarm via a sub-psionic link. This link is impervious to normal psionic attacks or disturbances. Annelid Swarm creatures seem to exist only as a living weapon, since their cells have a genetically programmed lifespan of no more than a few seconds. During these seconds, they are attracted to human tissue, as they frantically attempt to prolong their short lives with nourishment. The eggs from which these emerge often contain organs that might be extracted for useful purposes, unless the egg has been destroyed in combat.

Recommendation: The Annelid Swarm is best dealt with by avoidance, since the creatures will die soon after being hatched. Do not waste ammunition on them.

So they’re less stinging and more biting, like mosquitoes though I’m still calling them wasps. In a way, they’re kind of like the flying rats and lizards in PID: they fly in swarms, bite you a lot and cannot be killed. The difference is that Many wasps die on their own and both PIDs monsters can only be avoided by turning off your torch and stepping on explosive pods respectively.

In that Path of KAP Marathon mod I wanted to make, I would have had “carriers” which were basically the mulligans from the Binding of Isaac, which in turn seem to have been based on Halo’s Flood Carrier Forms. Carriers would be neutral and actually run away from the player but would get targeted by monsters: they’d explode upon death and release identical wasps to the System Shock 2 ones as I was inspired by all those games and the idea of Path of KAP was my own personal Binding of Issac story. Matching the PK weakness in System Shock, the Pinecone weapon would be the only thing that could kill them. Older, more decayed looking carriers would release more powerful wasp swarms with the “strongest rank” of carriers releasing wasps invincible to everything including the pinecone except being submerged in lava.

Act 3: Habe Quiddam – Operations: Cafeteria

Entering this new section of the level I find a sunken area with eggs hidden on the ceiling that drop worms on me like the Searching Head game in Fort Boyard.

One of the rooms here has a sim unit in it.

Since radio messages play automatically without requiring you to open them in the PDA unlike the first game, replaying the messages is the only way to see SHODAN’s face outside her reveal scene or FMV cutscenes with one exception later. Her character portrait here looks way too squished compared to her face in those other scenes so she looks goofy. In another room is Malick’s first chronological log where the Many begin compelling him to do their dirty work.

In the next room is the first exotic weapon of the game, requiring Research level 4 to study and Exotic Weapons skill 1 to actually use. Levelling up the former with the cyber modules I got for finding the chip and installing it, I check it out, backtracking for yttrium to use as glazing.


“You should go to this location and retrieve a device that your fellow crewmates have provided for us. It will allow you to slay more Many. Does that make you happy?”


Crystal Shard

Analysis: This crystal, principally of silicon but doped with germanium and other unknown trace elements, appears to have a resonant frequency very close to that of neural propagation. The crystal probably serves as a repeater for the psionic abilities of the annelid creatures. The crystal structure is composed of thousands of close-together crystal needles, attached together in a close-branching, nearly fractal tree.

Recommendation: The crystal’s amazing sharpness makes it a very dangerous hand-to-hand weapon.

This weapon is more powerful than the lightsabre but I likely won’t be using it this time: I have the laser rapier instead and I need the inventory space. Maybe on my next Navy playthrough.

This reminds me of the maggots introduction cutscene in Doom 3 with the half-dissected man crucified on the ceiling. Those ceiling panels are similar to the ones in that game.

Red monkeys are naturally a lot more dangerous but they are also weak against their own attack. In the mess hall, I destroy 2 turrets and a camera after backtracking to disable security. There’s eggs in the bathrooms including wasp ones. The wasps seem to get confused and fly into a wall, as if they’re running away from me.

By the serving hatch on the other side, there’s a long ghost sequence of Bronson and her men slaughtering innocent crew members she believes are part of the Many, even though the hybrids are bleeding obvious and none of them are ones.

A maintenance bot spawns during this sequence and shows up as it ends. Inside the kitchen is some goodies and a monkey.

Anyone else think those stove burners look more like switches in a build engine game? They do to me. Shadow Warrior did literally that in one level, though I can never remember if it was the main game or the expansion packs.

A log from Bayliss is by the window outside.

So it was Bayliss who tampered with my memory restoration earlier. Chances are we didn’t volunteer at all and SHODAN knew how good we were as a soldier so she chose us to work for her. She seems to be working with Dr Delacroix too though Delacroix seems to be either ahead of us or just behind. I check out the freezer for loot.

Looks exactly like your average Taco Bell or Applebees. J-rap musician & Hololive vtuber Karen Calanni could tell us all about that: she used to be a waitress in the latter and had a miserable time there. I don’t blame her for leaving that job in favour of livestreaming and following her passion: I would too.

An irradiated hallway leads past the pattern buffer back to the Xerxes core in the previous map. I pick up a log from Bronson as she slowly starts to lose it and several cyber modules from side rooms along the way. I find a large freezer with a red cyborg assassin hiding in it. Huge explosive containers fall from above in an avalanche and blow up. They keep coming until the cyborg is dead.

A log in here from Morris has him get 2 crystal shards of his own and is tasked by the Many with killing Sgt Bronson. He claims they’re very fragile but melee weapons in this game never break. Across the hall from the big freezer is a small games room with upgrade units, a cards table, a pool table and a small bar. I level up my strength and standard weapons in here: I want the assault rifle you can get at level 6.

Act 3: Thing What Kicks… – Operations: Firing Range & Barracks

There’s a laser turret down the hall and wasp eggs in the maze of machines and a large tank to my left when entering here.

Really does look like a Snoozelyn room bubble machine.

As System Shock’s answer to Marathon’s glancing controls, leaning returns from the first game and it’s still super useful for peeking around corners except now you can also lean forward to try and take things just out of reach otherwise, like searching eggs with less risk of setting them off. Deus Ex a year later would have similar leaning in it too. The pattern buffer is just beyond the turret. To the left is another turret, upgrade units and a firing range.

I remember this being the firing booths looking into an empty room. I’m pretty sure the targets are from Rebirth.

Outside the first barracks room is a log from Tommy to Rebecca, telling her they plan to pull a Ripley on this place which is to say escape and go into cryosleep while they await rescue or return to Earth. To the right past the pattern buffer is a vending machine that generates a unique machine when you hack it:


Originally developed as an adjunct to the replicator, the recycler contains a voracious colony of replication-enabled nanites, which will decompose just about any object into more nanites. Early incidents in which recyclers were used for disposal of bodies led to quick restrictions on what sort of items the recycler will accept.

Here’s a dramatic artist’s rendition of what using this machine to dispose of bodies would look like:

All that crap I’ve been collecting and caching by the elevator on every level has been so I can recycle it and turn it into more nanites once I finally got this recycler. There is a PSI power that lets you do this as well but sometimes one option is better than the other, with the strategy guide providing a handy table analysing when to use either. Prey 2017 expands on this and provides full size recycling machines you can drop random crap or unwanted items into and turn into raw materials of different types. Those materials are combined Bioshock U-Invent or Minecraft crafting table style into its own replicators to produce items, all of which have their own recipies/blueprints for you to find.

The System Shock remake combines the two by making recycling machines turn the junk into coins you can use in traditional vending machines, most of which are based on Bioshock’s ones. Certain items give more coins upon recycling but take up more inventory space, creating a dilemma about if you should turn them into scrap for space but get less coins or make even more trips to and from the recyclers.

I’ve compared this system to Another Code R’s gumball machine system. God I wish that game and its DS predecessor both came to Switch!

The other barracks have a log from Bronson declaring martial law with death as punishment for breaking curfew. There’s cyber modules at the end next to a farting egg.

Security bots in this game are based on the one from Robocop, but bulkier, use a laser cannon and recycle Thief robot animations. Pretty much all the robots except protocol droids in this game are direct upgrades to each other, told apart by their color, weapon and subtle changes to their chassis. Deus Ex’s high security bots are based on the ones in this game but with chainguns instead of laser cannons. The low security bots are still armed but resemble the serv-bots from System Shock 1 more. Marathon wise security bots are defence drones but a lot more cumbersome and inefficient.

The security bot and a pair of laser turrets were guarding a junction where the last red cyborg assassin is hiding.


“I am pleased. Transmitting cybernetic modules. Do not squander them.”


An audio log from Dr Delacroix nearby next to more modules hiding in the floor says that if the sim units are reprogrammed, SHODAN can divert power to a transmitter on level 5, using that will weaken Xerxes and allow SHODAN to grant access to the command deck elevator so people can reach the bridge and take control of the ship.

The middle path here leads to a room we can’t get in yet and down a ramp in the basement is a room with a surgical unit, another with 3 piles of worms and one with a red monkey on a table. There’s cyber modules down here.

Down a lift in the left path where the cyborg went before I killed it is a small brig. The forcefield bars are opened by little buttons next to the cells. 2 of them contain nothing but the third has a corpse with an alien implant I want and traps you inside with worms who come out of the corpse or from the ceiling. Destroying a junction box in that part of the ceiling disables the field and lets you out. I go and fetch some copper to give my new implant some spice.

I backtrack to all previous levels to recycle the junk I’d been collecting. I also stop by the armoury in MedSci crew section as I found the log with the code in that worm basement. The code is 98383. Inside is standard issue armour, booze, ammo, an assault rifle, an EMP rifle (the best energy weapon in the game and partially a huge waste of time), a stasis field generator, medkits and batteries.

Judging by the satellite dish, it looks like it should be a microwave gun but it’s just a stun gun that holds enemies in place like 2 of your PSI powers can already do. For the medium heavy weapon it’s just as useless as the dart gun’s tranquilliser ammo, stun gun and riot gun in the first game.

WormBlood Implant

Analysis: This implant is a high-powered blood filtering and reprocessing unit that acts to modify blood-borne annelid tissue so that it is benign in a human host. Because of the highly regenerative nature of these annelids, their tissue, in conjunction with this implant, can be used as a replacement for damaged human tissue. A small insertion port in the implant can be used to import annelid tissue for this use.

Recommendation: While under the effect of this implant discarded annelid tissue, such as that found in worm piles, can be used for a regenerative effect. Use of annelid tissue in such a fashion while the implant is not powered is strongly discouraged.

In other words, this is the implant that lets us eat those worm piles for health. I love this implant! It’s so useful. Just don’t stand on the worms especially with the implant removed or unpowered: as said before, normally the worms poison you if you touch them. Also, be sure to fill any beakers you find with worms before you eat them as doing so removes the pile. Worm clusters in beakers are worth a lot of nanites when you recycle them.

Through a broken door at the end of the hall is a security station with a linear sim unit in it. Bronson is here slumped against the wall dead. A log from Diego is in the desk and some ammo, a multitool and a laser pistol are in the footlocker.

Coming in here is worth it as I think that assault rifle on the left doesn’t ever break due to a glitch. Others like the one in the MedSci armoury aren’t so lucky.

Fusion Cannons require level 6 in heavy weapons to use and they use rare prism ammo, also used by the stasis field generator/stun gun. It’s basically the BFG 9000 from Doom. Through the maze of machines and the bubble machine is a hallway where I play peekaboo with a laser turret. Malick left a log on the floor here.

Cutting the cryptic crap, he’s booby trapped the interpolated sim unit in this area to release spiders when you get too close. There’s also wasp eggs over the ladders leading down to it. Finally after killing the 5 or so spiders down here do I find one of their organs I can research. Boil it in molten iridium.


“This is Xerxes. At 0200, there will be a poetry reading by Protocol Unit T892/2 in the Deck 5 commons area. Please bring any authorised material that you wish to be read by T892/2.”


Do the Many even care about human poetry? The Gravemind in Halo does as he says to Cortana in one of the books that the vast number of poets the Flood has consumed is why he speaks in that weird constantly rhyming way he does, dropping the rhymes just to tell her that.

SHODAN directs me to deck 5 as she anticipates her revenge on the Many. On my way back I use my new implant to eat the worms in the basement near the locked computer room. Normally it’s silent or uses a regular pickup noise but the mods make a slurping, chewing sound play instead.

Mmm. Meatnoodles.

Arachnid Organ

Analysis: This creature’s internal systems are both distributed and redundant in a way that suggests intentional design, or evolution in a very dangerous environment. What serves as its nervous system uses a significantly larger amount of energy than a human’s, so the creature’s tissues are correspondingly more energy resistant. The creature’s metabolism allows for a boost of hyperkinetic activity, while allowing it to remain normally in a dormant state, and presumably allowing it to exist for a long period of time without nourishment.

Recommendation: Using energy weapons against this creature is not recommended.

Normally I like spiders and consider them a helpful creature who kills actual vermin like flies, moths & wasps (unless said spiders are poisonous to humans), but kill those ones with fire. They’re weak to it as well as anti-personal rounds. Next stop: level 5, where we see two familiar objectives from both PID and Marathon, one returning from the first game.

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