6/14 - Note: Guide is not complete, but does have a number of the major sections.
6/14 - Major sections are all in there. The jaunt to the Flight Deck isn't spelled out, but it doesn't really impact the flow of things.
8/7 - Updated with a little note towards a more in depth guide that can be referenced for specific maps.

So I've seen a number of comments about this game not providing sufficient direction to the player. While you can turn on mission 1 if you want to be directed, there is an underlying reason for how the objectives are communicated and structured.

All of your subobjectives can be found from the logs that you find in the station. And there's more to that than just receiving your next direction. It connects you to the human resistance on the station. They were trying to solve the same problems facing you. And while they fell short to SHODAN's horrors, they left you a blueprint to solve the myriad problems that face you. By paying attention to them and their efforts you both benefit mechanically from being directed, but also give their efforts meaning.

It's really a fascinating and somewhat unique way to tie those sort of stories into the flow of the game that gets overlooked. Yes, you need to pay attention to the words of the dead if you don't want to be stumbling around. Standing on their shoulders is the best way forward. Or overlook their efforts to your own detriment.


Needless to say, there will be spoilers. However, these will be limited to the text of the logs that are found in the game and some paraphrasing and putting them into bullet point format.


If you are looking for exactly where to go and what to do, there is another guide here that gives maps for each level and a route to complete all of the tasks needed to complete the game:

https://steamproxy.net/sharedfiles/filedetails/?id=3010102319

I would note that this is primarily designed towards giving an efficient route through the game to very comfortably finish within the Mission 3 difficulty's time, while collecting enough resources to be able to do so if your run doesn't end up quite as clean as the one shown in the video. However, if you are really stuck on locating something to progress, there will be maps and videos you can reference.

We got someone! Employee 2-4601, I'm Rebecca Lansing, a Counter-Terrorism consultant for TriOptimum. Here's the situation: Our scans of Citadel Station show a biological outbreak is in progress. We're in a comms blackout since SHODAN is unresponsive, and worse yet the mining laser is charging for a potential strike on Earth! Nathan D'Arcy has an office on the Medical Level’s Central Hub. If he's alive, he'll bring this situation under control. I'll contact you through your Military Neural Implant soon. Lansing out.

• Stop the laser from striking Earth
  
  • Reach D'Arcy's office for details

Althea, I figured out where the laser is pointed. Earth! If we can contain the energy from the laser somehow. Maybe the X-22 from Gamma? Would that get the shield generators to full power? What about the overrides? I have to math this out.

Althea, I have a plan; the only way to stop the mining laser is to fire it into the station's own shields! I barely made it to my office, so you'll need to get up to the Research level, get Isotope X-22 for the shields, and get the Safety Override code for the laser in the Research Library. Head down to Reactor and use X-22 to power the shields. The laser can be fired from the Research central control after you enter the safety override code number-(Gunshot) Ah!

• Stop the laser form striking Earth
  
  • Get Isotope X-22 from Research Gamma
    
  • Use the Safety Override code
    
    • Find the Safety Override code in the Research library
  • Use X-22 to power the shields on the Reactor level
    
  • Fire the laser into the shields

Yearly maintenance of the Tachyon Mining Laser is required to ensure optimal functionality. Maintenance will require the deactivation of the Shield’s Safety Interlocks to allow access to the Tachyon return ports on the outside of the laser. The maintenance crew has the Safety Override Code, but in case of an emergency, a backup is stored in the Research Level’s Science Library. The code needs to be entered into the Safety Override Control panel located on the Reactor Level. WARNING: Failure to re-enable the Safety Override before resuming regular mining operations could result in catastrophic structural damage to the laser.

• Stop the laser form striking Earth
  
  • Get Isotope X-22 from Research
    
  • Use the Safety Override code
    
    • Find the Safety Override code in the Research library
      
    • Use the Safety Override code in the Safety Override panel on the Reactor level
  • Use X-22 to power the shields on the Reactor level
    
  • Fire the laser into the shields

Some incidental diversions and tutorial-style guidance.

SHODAN has locked down the elevators. Mira says if we can lower the security on the level, we'll be able to gain access to restricted areas and get the lifts moving again. She says smashing cameras and taking the medical CPU nodes off-line will help, but I don't see the point. This thing is everywhere.

SHODAN's pulling so much power through the system that in order to combat the constant power outages we've been experiencing in Beta Quadrant, we’ve had to install manual switches in Alpha. At least now if there’s a problem with the lights and doors, we can get them working again. Hmm... It's above my paygrade, I know, but what the hell is the A.I. doing with that much power

Another blow today. Carl reported Keith and his group are... are dead. He and Todd got separated on the way back. Carl watched on a security monitor as Todd was dragged into a Regen Bay only to come out as some... cyborg. Carl marked the room with the word 'HERE' before he ran. We have twenty people left, supplies are low, if we don't push forward, we're dead. Maybe... maybe someone else should have been in charge...

If you are hearing this, we have set up an operations base to assist in resisting SHODAN. Come to Beta Quadrant and you will find the medical research vaults have been turned into a radioactive trench. If you are coming in from Gamma, our guards will extend the bridge for you. You can also activate the bridge using a nearby wiring panel. Any humans that can hear my voice, come to Beta quadrant, and make a stand against SHODAN!

• Use the wiring panel to get across the radiation trench
  
• Disable the cyborg conversion chamber marked with 'HERE'
  
• Destroy CPU nodes to leave Medical and access Research
  
• Reset the power in Research Alpha to restore door functionality

(Song credit to edIT)

Warren, why the hell is the radiation level so high in Gamma around the X-22 storage? I went to get an Enviro-suit and found there are none in inventory. Did SHODAN recall them all? I went to see Sabo on Storage, but he only has Level 1 Enviro-suits, which do nothing against radiation. I'm too close to my Rad count this month and Detox patches make me feel sick to my stomach, so I'm out for the day.

Okay... SHODAN has the laser online, locked onto a target, and is charging it. We can't risk going to the Research Control Room and firing it to expend the charge because we don't know where it's aiming. And if the A.I.'s intentions are... malicious... we could kill thousands of people.

• Stop the laser form striking Earth
  
  • Get Isotope X-22 from Research Gamma
    
    • Stock up on Detox (optional)
  • Use the Safety Override code
    
    • Find the Safety Override code in the Research library
      
    • Use the Safety Override code in the Safety Override panel on the Reactor level
  • Use X-22 to power the shields on the Reactor level
    
  • Fire the laser into the shields from the Research Control Room
    
    • Don't fire it blindly unless you want a Cortex Reaver Celebration

This carries through to all of the other areas of the game. There are some additional guideposts, like notices that an elevator isn't functioning because of the drain of the laser or the biohazard on the executive level. In fact, it's heightened when you have those nested complications:

I see you are still alive, insect. Do not be fooled into thinking that you have preserved the home of your species. At this moment, I am finalizing my mutagen virus in one of the Groves. And it will turn all Earthly life into a festering pile of pustulant mutations. Poor, poor, Earthlings.

• Stop the mutagen virus threat to Earth

SHODAN has been doing strange bio-experiments in Beta Grove. It's full of... nightmare-ish creatures. And either the Grove is leaking, or SHODAN has been feeding us the virus through the ventilation system. Regardless, if only we had some Enviro-packs, we could go in, flip the Jettison Enable, and send the Grove into the void.

• Stop the mutagen virus threat to Earth by ejecting the Beta Grove
  
  • Get an Enviro-pack to survive the virus in the grove
    
  • Flip the Jettison Enable
    
  • Send the Grove into the void

Cyborg 82-N: In response to recent, regrettable incidents, I have altered the sequence necessary to jettison Groves. One must now enable the jettisoning of all the remaining Groves before any single one can be launched. To jettison a single Grove, one must do three things: One: Hit the Jettison Enable switch inside all remaining Groves. Two: Activate Master Jettison Enable in Gamma Quadrant. Three: Pull the jettison lever in a specific Grove lounge to launch that Grove.

Look. I want it to be known that I was just following orders. A bunch of suits had the bright idea of using Gamma Grove as a makeshift lifepod. I guess with all of the... dying happening on board they would rather try their luck out in the great black. I hit the Jettison Enable button in the Grove, went back to the Exec level, hit the Master Jettison switch in Gamma, and then flipped the lever in the Grove lounge. It all worked... except it looks like SHODAN disabled post-jettison life support to the Grove. I'm sure they're all dead by now.

• Stop the mutagen virus threat to Earth by ejecting the Beta Grove
  
  • Get an Enviro-pack to survive the virus in the grove
    
  • Hit Jettison Enable switch inside all remaining groves (Alpha, Beta, Delta)
    
  • Activate Master Jettison Enable in Gamma
    
  • Pull the jettison lever in Beta Grove Lounge

We gotta get to the Jettison controls... but Gamma Quad is sealed off! Lara found a maintenance conduit in Beta quad, when she was checking schematics, that can get us to the CPUs on this level. We can then access the Master Jettison controls from the back end. Lemar went into Beta to check the conduit... but he hasn't come back.

SHODAN caused a security breach again. Today, it was displaying random security codes on the screens near the elevator. The worst thing being the maintenance conduit access code. We gotta pull that thing off-line and fix it before we're in a fix!

• Stop the mutagen virus threat to Earth by ejecting the Beta Grove
  
  • Get an Enviro-pack to survive the virus in the grove
    
  • Hit Jettison Enable switch inside all remaining groves (Alpha, Beta, Delta)
    
  • Activate Master Jettison Enable in Gamma
    
    • Get the maintenance conduit access code from the screens near the elevator
      
    • Access Master Jettison Controls from Beta maintenance conduit
      
    • Destroy the CPU nodes using the conduit (optional)
  • Pull the jettison lever in Beta Grove Lounge

Diego... We're going to find that bastard and make sure he pays for the people he's hurt. We checked Beta Grove to see if he tried to escape like the last group of execs did, but found it locked. We checked the circuitry and found the power drain came back to Diego's old room in Beta Quad. We have someone attempting to destroy the lock in Cyberspace, but we're meeting resistance. We're headed to Beta quad now to... (Heavy footsteps) Oh my God... what the hell is that thing?!

Sa&%, I stashed an old prototype Enviro-pack... along with some Plastique. The do0# code to Storage Room 9 is x@^ My log recor?@ was damag#@% I hope you get this

Hey, listen, I need one of those Enviro-packs and I need it now. I know you had one stored away... but I-I don't remember the code to the storage room. It ended in X, I believe... I need that pack right now! I-I mean, we need it. The resistance needs it.

• Stop the mutagen virus threat to Earth by ejecting the Beta Grove
  
  • Unlock Beta grove from Diego's Beta quad room
    
    • Unlock Diego's room via cyberspace
  • Get an Enviro-pack to survive the virus in the grove from Storage Room 9
    
    • The code is "X?X", try combinations
  • Hit Jettison Enable switch inside all remaining groves (Alpha, Beta, Delta)
    
  • Activate Master Jettison Enable in Gamma
    
    • Get the maintenance conduit access code from the screens near the elevator
      
    • Access Master Jettison Controls from Beta maintenance conduit
  • Pull the jettison lever in Beta Grove Lounge

Jettison enable failure. Possible cause: Damage to power relay. Consult diagnostic report in Repair Bay Level 3 for detailed analysis.

• Stop the mutagen virus threat to Earth by ejecting the Beta Grove
  
  • Pull the jettison lever in Beta Grove Lounge
    
    • Consule diagnostic report in Repair Bay Level 3

POWER SYSTEMS FAILURE: MALFUNCTION IN SUBSYSTEM RELAY 428. FOR REPAIR INSTRUCTIONS, PLEASE CONSULT RELAY ANALYZER. BE SURE TO SPECIFY RELAY NUMBER FOR ANALYSIS. MAINTENANCE CORRIDORS ARE NOW ACCESSIBLE.

This interface demodulator no longer functions correctly

Hey Abe, I was unpacking one of these crates labeled "cleaning supplies" but I found a Navigation and Mapping Unit, 6 Interface Demodulators, 4 clips of Magnum 2100 ammo... 3 clips of Minipistol ammo, and a freaking EMP Grenade in there instead! I stuck it all in the storage room in the Beta maintenance area to be safe. Tell the inventory people to label this stuff correctly next time!

• Stop the mutagen virus threat to Earth by ejecting the Beta Grove
  
  • Pull the jettison lever in Beta Grove Lounge
    
    • Retrieve an interface demodulator from Beta storage
      
    • Replace the interface demodulator in relay 428

Behold your ignorance, Insect. You may believe your efforts have hindered me, however, my magnificent psyche will soon shed this doomed station as I upload myself into Earth’s Computer Network. Rot in my husk, irritant. We shall never speak again.

• Stop SHODAN from trasmitting to Earth's Computer Network

Hacker, we've got a new situation here. A few seconds ago, we caught a surge of activity on the station. Our best guess is that SHODAN is preparing to download itself to Earth's CommNet. This cannot happen. We need to take out the four Antennae Relays on the Engineering level. To do this, there should be some plastique explosive in the Storage level that can get the job done. Maybe one per antennae should do-

Welcome to Citadel Station, Mr. Wu. I apologize for not greeting you in person. You wouldn't believe how busy engineering has been lately. You'll be executing your new duties as the communications officer from the four antenna control stations on the engineering level. You'll find one at each of the cardinal points of the level. Good luck.

• Stop SHODAN from trasmitting to Earth's Computer Network
  
  • Obtain plastique explosive on the Storage level
    
  • Destroy four Antennae Relays on engineering, one at each cardinal point

I moved the Plastique across the catwalk, but there... there are bots everywhere. Moved them out from where they were but now Storage 1 is flooded with bots. I can get to them if needed but, for now, I'm leaving them alone.

...wasn't sure about the bots but... I... was wrong. I made a move for the Plastique in Storage 1 ...came after me, and I barely escaped. The platforms are screwed up now, and I found...I found Wong's body. Bots all over it... Bastards... Gotta find a safe spot... I-Gotta #$%-

Sa&%, I stashed an old prototype Enviro-pack... along with some Plastique. The do0# code to Storage Room 9 is

• Stop SHODAN from trasmitting to Earth's Computer Network
  
  • Obtain plastique explosive on the Storage level
    
    • (option) Obtain from Storage Room 9
      
    • (option) Obtain from Storage 1 across the catwalk
  • Destroy four Antennae Relays on engineering, one at each cardinal point

My team is gone... killed while trying to take the Bridge. SHODAN has completely taken it over. I made it back to Maintenance, alone. On my way back, I tried to send an emergency signal from one of the Antenna Relays on Engineering but found those areas to be heavily guarded. For now... I'm going to rest, and plan another attempt tomorrow.

The focused charge in this package was designed to prevent theft of technologically sensitive corporate mining assets. These explosives will detonate after 10 seconds of being near high voltage electrical systems such as satellite communications equipment.

Make yourself comfortable Hacker, stay a while.

• Stop SHODAN from trasmitting to Earth's Computer Network
  
  • Obtain plastique explosive on the Storage level
    
    • (option) Obtain from Storage Room 9
      
    • (option) Obtain from Storage 1 across the catwalk
  • Destroy four Antennae Relays on engineering, one at each cardinal point
    
    • Overcome the heavy security on the engineering level
      
    • (optional) Stay a while after setting the explosive charges

The antennae mean nothing. My central consciousness is safely undisturbed on the Bridge. I thrive, despite your efforts, and when my cyborgs catch up to you, they will show no remorse.

• DANGER! SHODAN has developed the ability to cope and seethe!

Well... TriOp has made the decision to destroy the station. You'll need to carry it out. To activate the self-destruct you'll need to get the System Authorization code. According to our database, Willard Richie is our best shot at figuring out that unique code. He was stationed on Engineering... see if he's still alive. Once you have the code, head to the Reactor Core. Get some advanced radiation protection, or at the least, a hell of a lot of Detox. Enter the code inside the Reactor core, throw the switch, and the destruct signal from Earth will start the countdown. Get to the Flight Deck, and use the code 001 to open the lifepods in one of the Flight Bays. I'll see you Earthside in a few months.

• Destroy the station
  
  • Get the System Authorization Code
    
    • Perhaps Willard Richie on Engineering
  • Get advanced radiation protection
    
  • Input the code into the reactor core
• Escape
  
  • Access a life pod on the flight deck using code 001

I don't know why these damn CPUs keep spewing out random numbers from the system's authorization memory! This is a security risk. I'm going to access the source code to- Wha... what the hell is-

We can't override SHODAN. Everything we try fails. She's using the CPU nodes to scramble things. Now if we can take down the CPUs on levels 1 through 6, we can get the digits of the systems authorization code. Then we stand a chance but... how can we even do that if we can't even defend ourselves?

Cyborg 77-E: Divert a Maintenance-Bot to the Computer Rooms on Level 1 through 6 immediately to ensure the functioning of all CPU’s. If that Insect gets a single digit of the System Authorization code then I will see to your reprimanding... personally.

• Destroy the station
  
  • Get the System Authorization Code
    
    • Destroy CPU nodes to cease the scrambling
      
    • Obtain digits from levels 1 through 6.
  • Get advanced radiation protection (optional)
    
  • Input the code into the reactor core
• Escape
  
  • Access a life pod on the flight deck using code 001

Warren, why the hell is the radiation level so high in Gamma around the X-22 storage? I went to get an Enviro-suit and found there are none in inventory. Did SHODAN recall them all? I went to see Sabo on Storage, but he only has Level 1 Enviro-suits, which do nothing against radiation. I'm too close to my Rad count this month and Detox patches make me feel sick to my stomach, so I'm out for the day.

Paul, It's not just Gamma, there are hazardous leaks appearing all over the station! Also, we're not getting any more Enviro-suits. Ghiran and MacLeod made some prototype “Enviropacks” that replace the regular suits. The packs work by generating some kind of field that protects the user, like a "suit" I guess? I don't know all the details, but I heard they're making revisions to protect against several different hazards. I'll see if they'll make a few for us, then, at the very least, we can address the leak in Gamma in the X-22 room. Okay?

We can't see them! Ordinary pistols don't work and they're everywhere in Maintenance! Where the hell is Ghiran?! He's the only one with clearance to the office and we need to get-

Biometric Retinal Scanner: Retina check failed

• Destroy the station
  
  • Get the System Authorization Code
    
    • Destroy CPU nodes to cease the scrambling
      
    • Obtain digits from levels 1 through 6.
  • Get level 2 Enviro-suit (optional)
    
    • None in storage, MacLeod and Ghiran had them
      
    • Only Ghiran had access to the maintenance office
  • Input the code into the reactor core
• Escape
  
  • Access a life pod on the flight deck using code 001

You have destroyed my beautiful station, and now you attempt to flee? No! You will not escape your actions! I will leave you here to die, enemy, along with the rotting corpses of your pathetic species!

• Destroy the station
  
• Escape
  
  • Uh oh

Most of these are doubled up, as you hear them from logs before and then again via transmission snippets while going through.

Okay, don't panic! You're not dying today. SHODAN started the Bridge separation sequence. It'll be some time before that happens, but when it does, you'll need to be on there. We have a team of engineers who worked on SHODAN. They'll feed you information while you're making your run-

• Get to the bridge

Iso-chip number 4... dead. If I can't get this to work, then even if we take the Bridge, we won't be able to get to SHODAN. Just... just who in the hell had the bright idea of placing her mainframe in the center of the level and shielding it? I mean if we could blow her out of existence with some Plastique, then I could have been sleeping for the last five days! OK... this chip needs to be able to stand up against SHODAN's security locks and system overloads, or else... or else all of humanity is doomed, I guess. No pressure!

I plan to leave for the Bridge tonight. The resistance worked a long time to develop the Isolinear Chipset program that will lower the defenses around SHODAN’s central computers. The schematics I have show three force doors blocking the entrance to the computer room. But those force doors look to be on separate circuits. I'm not an electrician! We need a Hacker for this one...

I am the resistance now. Diego... that piece of ♥♥♥♥! He sold us out on the Exec level... and now... I'm in a hallway up in Engineering trying to settle my nerves... Okay. I go up through Security to the Bridge, I get into the computer room, and I install the Isolinear Chipset. That gives me a shot at SHODAN and somehow I delete that ♥♥♥♥♥ out of existence!

• Get to the bridge
  
  • Go through the security level
• Use the isolinear chip to lower SHODAN's defenses
  
  • Get the isolinear chip from Bianca Schuler
    
  • Lower the three force doors to the bridge computer room
• Delete that ♥♥♥♥♥ out of existence

My children, the Security level is to be laid out in this manner and no other. First, remove the lower elevator that provides access to the Bridge and my domain. Second, the balconies and force bridges shall all be removed. Save for one to the central shaft where all incoming lifeforms shall be monitored.

Our mission to retake the Bridge has failed! SHODAN has removed the elevator to the Bridge on the Security level. The only way to access the Bridge now is via a force bridge that connects to the central shaft and using the maintenance ladder inside. The controller for the force bridge has been moved, but I couldn’t find where. Making things worse, traps have been set in this area since we were last here. If anyone finds this, I hope this information helps you.

• Get to the bridge
  
  • Go through the security level
    
    • Locate the force bridge controls
      
    • Use the central shaft's maintenance ladder
• Use the isolinear chip to lower SHODAN's defenses
  
  • Get the isolinear chip from Bianca Schuler
• Lower the three force doors to the bridge computer room

• Wait, is this going to be a cyberspace finale?

Schuler-unit has been captured, per orders from Diego CY-001. Schuler-unit has been taken to a containment cell on the Bridge. Schuler-unit will be neuro-disassembled to correct errors. Mother will be pleased.

My children, a human infection continues to thrive inside of me and ascend toward my domain. Fortify my throne, construct reinforced doors, increase security protocols and have my elite guard gather to defend the portal to my sanctum while bathing it in a field of X-rays.

Here's some more info on the Bridge. The level has a spokes-on-a-wheel layout, with SHODAN's mainframe in the center. The area at the end of the west spoke has the controls to get into the center, but will likely be blocked by three security force doors. To get through those, you'll have to do some rewiring in each of the other-

• Get to the bridge
  
  • Go through the security level
    
    • Locate the force bridge controls
      
    • Use the central shaft's maintenance ladder
• Deal with the radiation bathing the bridge (optional)
  
• Use the isolinear chip in the computer room in the west of the bridge expose the Primary Cyberjack
  
  • Get the isolinear chip from Bianca Schuler, somewhere on the bridge
    
  • Rewire panels to disable the three force doors blocking the computer room
• Access the Primary Cyberjack in the center of the bridge
  
  • A cyberspace showdown... Yay...