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 Cell of Empireo "Walkthrough"
 
[This is me basically summarizing the guides from here and putting them in one singular place for my own reference (I cut out a bit, so please go check the guides on your own if you'd like). This has what you should do in every chapter to reach S end, & includes Kanou flag. But it also tells you exactly what you should do and has all the puzzle solutions, so if you'd like to figure out what to do/solve the puzzles on your own, I suggest you don't read this, and instead read this page, which just gives you hints for the three puzzles without giving you the answer. However, I will warn you that a lot of things in CoE are easily missable once you pass certain points and it's very easy to get locked out of the best ending. Do whatever you think is best.
Highlight to read.] 
Some notes for those who want the best ending. When you have the chance to talk to allies or party members, talk to them as much as you can right when they become available. Don't wait.
When you see a yellow book on a bookshelf, it's an important book. Read it. (there are other books not marked yellow, but that's how you spot readable materials from a distance.)

For chapter 4: 
  • Get the protective charm from Karen when you talk to her. [not 'needed' but will save you from one singular death if it happens]
  • Get the B1F map from the east hallway wall. [again, not 'needed' but useful to have a map]
  • Get the flashlight from the top cardboard box in the nap room. You will lose sanity if you check the other one.
  • Talk to the researcher in the sink room. He will tell you about a blue card. After that, go back to where Yanagi is, talk to her, and she will give it to you.
  • You can use the blue card to get into a room with a lot of machines [first door you see on the top when you enter the west hallway]. There is a door in the back, locked with a 4 digit password. The password is 5326. Go into that room and pick up the metal pipe in the center of the room.
  • Use the metal pipe to pry open the door in the hallway that's slightly open. You will find the green card in that room.
  • This will let you enter the shower room (the door in the back of the break room). In the shower room, check the washing machine on the right to find a key. Go into the shower room farthest on the right and you'll see something shining in the drain. Pick it up. [Something will jump out from the stall next to you once you leave, but it's honestly not all that fast & if you walk straight to the exit you should avoid it without much difficulty.]
  • Go to the women's bathroom and give the ring you just got to the woman blocking your path, and she will leave. Keep in mind if you talk to her too much without having the ring, she will kill you.
  • Check the stall closest to you on the right side of the women's toilets. You'll find AA batteries on the shelf there. Use them.
  • Use the key you found to open Warehouse A [bottom door, west hallway]. You will find a gun in the next room behind it. 
  • Go back to the room everyone else is in. This will trigger an unskippable chase scene. Be careful. Unlike many of the other monsters here, this one can chase you through doors and is fast (there's also a lot of flashing red effects & static sounds when it does, so turn your screen brightness down/be warned if you're sensitive to that). You will see the door directly across from Warehouse A open. Run in there. Do not run into Warehouse A, despite Atou saying it seems like a good hiding place. He's wrong and you will get jumpscared and die if you turn your flashlight on. 
  • Examine the corpse in the middle of the room in Conference Room B. Kanou will disappear. When you leave Conference Room B, it will trigger another unskippable chase scene (again, warning for the flashing effects and static). Run to the boiler room. (north hallway, door on the top right.). There's a tank fallen to the floor in the boiler room. Push it in front of the door by interacting with it from the left, rather than trying to go around. Keep in mind that you will die if you don't do this quickly enough.
  • Go to the garbage disposal room. There's a shelf in the back that you can move. (turn your flashlight on high). A key will fall off of it. Use it to unlock the room next to the stairs [since you don't have Kanou's key at this point, use the hole]
  • There is a stepladder you'll find in that room. Take it, go back to the room where debris is blocking the way, and use it to climb the debris.
  • [Side note. There is a woman you'll find in the living quarters, who asks you to find her friends. To do this, you'll have to go to Conference Room A, but don't pick up the yellow card you find there before you go back and talk to her or she'll die. This is completely optional & unrelated to the Kanou flag. She'll give you a photo if you successfully do this that can be used to reduce corruption in chapter 4.
  • Pick up the yellow card in Conference Room A. Then examine the corpse in Conference Room B with your flashlight on high to get the notebook.
  • To trigger the Kanou flag, you will need to backtrack to B1F, to the analysis room before Kanou rejoins your party. There's a door that was previously locked that you can unlock with the yellow card. There's a journal in there. Read it. [Keep in mind that you will not be able to trigger the Kanou flag if you read the journal once Kanou's back in your party. Triggering it will change some dialogue in chapters four, five, six, and seven.]
  • Kanou is in the specimen room [door in the north hall, directly across from the boiler room.] Go there and get him. He will give you the red card.
  • There's a shutter that's open a crack in the B2F west hallway. Kanou can pry it open for you. Go in and you will see a flashback, and you'll find a USB cable there. Pick it up.
  • There's a door across from where you got the USB cable [the lab, not the living quarters]. In the back of that room, you'll see a HDD. Pick it up, then you can go back to Conference Room B to use the laptop there to read/listen to everything on them.
  • Once you've done that, head back upstairs to the analysis room and look at the journal with Kanou to get half of a note. 
  • Then, go to the specimen interview room (room across from the cell you started the chapter in) with Kanou, and he'll help you guess the four digit password for the room itself. This is randomized every game, but if you want to skip playing a guessing game with Kanou, stand directly in front of the door, then turn to face down and examine the wall in front of you. The code is written there.
  • The other half of the note is inside the room, in the cabinet on the top right. Don't take too long to find it or Kanou will kill you.
  • [you can get the two halves of the notes in whatever order you like.]
  • The password you'll get from the notes is 6957. Use it to unlock the garbage disposal room.
  • [Sidenote: use the dead flashlight and you'll take the dead batteries out of it. When you get to the garbage disposal room with all the monsters in it, and Kanou is in your party, use the dead batteries. He'll throw them at the monsters, scaring some (but not all of them)away. This is also optional, but given there's a chase scene later on that requires you to run through this room, it'll make things easier.]
  • For those sensitive to flashing: the end of chapter 4 chase/escape scene features heavy use of the red flashing sound effect and alarms. [The red flashing screen effect is used a lot throughout the whole game, but it's an extended scene . It's less bad in future chapters, but I'd advise you to turn your screen brightness down if that bothers you.]
  • For the chase scene, just get the gun from the researcher and run down the corridor to the barrel. Keep enough distance between you and the monster, or you won't be able to shoot it and you'll die. Good luck.
Chapter 5 doesn't have any puzzles, but I highly recommend you talk to everyone as much as you can if you want the best ending.


For chapter 6:
  • Get the map from the man in the 3F break room. This is optional, but it's nice to have a map.
  • Go to the library on 1F, and examine the door.
  • The key you're looking for is in the 1F break room. You can get it whatever way you want, but using Atou's powers will increase corruption. (You can just ask the guy for it. It's fine.)
  • Talk to Aiba as much as you can.  
  • When you leave the library, there will be a listening in minigame. If you do it perfectly, you'll be able to hear their whole conversation. Try your best. 
  • The door is being guarded. You can either use your abilities on the purple planters or push the vase over. Keep in mind, using your abilities on the planters increases corrosion rate, but if you push the vase over it will be unusable.
  • Talk to everyone in the room as much as you can. Everyone is stressed, so I would highly advise trying to be as understanding as you can and try to find out the reasons for certain things happening. Please also keep in mind that harsher dialogue options will affect a hidden time limit later in the chapter. 
  • You will enter a state of confusion after what you see after leaving the room. You can either go upstairs to the men's bathroom and use the vase there (if you broke the one earlier) or use the one close by (if you didn't). Don't take too long to find the vase or you will run out of stamina and die. Don't go down the stairs while in a state of confusion either, or you will also die, but in a different way.
  • Get a survival knife from the man in the kitchen on 1F. You can also get it by pulling it out of a body in the 3F break room, but that will spawn a monster and will also cause you to be attacked by the man in the kitchen on 1F if you talk to him, so I advise against it.
  • Go back and talk to Aiba. Again, as much as you can.
  • You'll see that a book has fallen on the floor of the library. Read it.
  • Use the door between the library and break room. It will lead you to a corridor. There's a map in there, so pick that up. (You don't need to. However, again, it's more convenient.)
  • Go to the 1F confessional to get the code number note.
  • Use this and unlock the box in the 1F reception office. The PIN is 6841. You will get two keys. One is to the reception room to the right of the office. Go in there and pick up the note on the floor. Make sure you read it.
  • Aiba will have asked you for bandages when you talked to him earlier. The bandages are in the 3F women's dorms, in the cabinets. Go back to him, and he'll ask you for crutches. Those are in the 1F warehouse. 
  • Pick up the stick in the locker in the 1F toilets, and you'll be able to use it to take the key out from under the monster in 2F. You can then enter the room and take back everyone's things.
  • Make sure you've given Aiba the bandages and crutches before you take everyone's things back. 
  • Take the old cellphone to the lab on 2F (the one that was unlocked with the key you got from the reception desk) and charge it.
  • Go back to the library. You'll see that Aiba's gone.
  • Return to Yanagi and Kurachi. During the scene that follows, pick up the sparkling piece of debris on the ground, then escape the room. Don't take too long. (Yes, you can die here too if you do.)
  • At the point where Karen runs upstairs, use the stairs up to 2F in the church to intercept her, not the ones by the bathroom (also, don't take too long, again.)
  • Run to the 1F confessional room. It will be unlocked. Go inside. The solution to the lights out puzzle is 'top left (7 key) top right, (9 key) center (5 key) and bottom center (2 key). This is also timed (not visibly, but if you talk to Karen by the entrance and she isn't telling you to hurry anymore, she's just giving you a horrified look and going '......' you have taken too long) , so be careful. Your answers to Yanagi earlier will affect how long the timer goes for. Jabuchi should tell you about a hidden door at the end of this, if you've done it right.
  • Use the survival knife on the arm to get the finger. 
  • After this, go to the lab and get the phone back. It should be charged now. The password is 'tina'. Or rather, ティナ. 
  • When you're back in the room with everyone, talk to everyone as much as you can (again). Karen will give you a key, and some of Kurachi's dialogue should change if you got the Kanou flag. 
  • Now that you have the key, you should be able to unlock the room with all the books. Read the yellow ones. (You can read the rest, if you'd like, but those give interesting information. You need the one about 'origins' to unlock S ending.)
  • Go to the hidden room on the fourth floor that Jabuchi mentioned, and check the curtain. You'll find a door. Inside the room is a diary. Make sure you read it, don't just pick it up.
  • If you're on S route, the flashback at the beginning of chapter 7 will change and you'll be able to leave the room instead of just overhearing people outside the door. 
For chapter 7:
(One warning about Chapter 7: there's a hiding minigame where the screen goes completely black later on in the chapter. It's not too difficult, but keep in mind that if you fail it there will be a startling image flashed on the screen (monster).) There aren't really any other things like that in this chapter besides this minigame.
  • Examine the plant in the corridor (on the Moon Floor) to get a plant fragment. 
  • Check the orange book in the control room to get a certain photo (you need this for S end) Also check the analysis machine in the control room, or you won't be able to pick up the handkerchief later. 
  • Go into the storeroom on the Moon Floor and check the shelves to get hydrogen peroxide.
  • Check all the rooms for yellow books. You need to find and read Kazue Enomoto's reports number one through six (and then get her disk once you read the sixth) for S end. Three reports are on the Moon Floor, two are on the Star Floor, one is below the courtyard. 
  • There are also five rats that you need to interact with in order to get flashbacks. You need to collect them all for S end. One is in the courtyard, there's one in isolation cell A & B, one is in the control room. You can do this/collect the reports in any order, but make sure you finish these things before you make the call on the stairs.
  • The elevator puzzle answer is up 4, down 5, up 6, down 4, up 6. 
  • Examine the toilet on the Star Floor to find a key.
  • The password is 'Stella'. 
  • The vision blocking the door will disappear if you use the hydrogen peroxide you collected earlier.
  • Check the book that's fallen on the floor in the cultivation room to get a flower tag. A chase scene begins when you pick up the flower tag, so run to the elevator. There's some mild flashing, so turn your screen down just in case, but it's not as bad as the flashing in ch4. 
  • Pick up the bloody handkerchief in the corridor on the Moon Floor.
  • Pick up the ballpoint pen (shining object) next to the box near the elevator on the Moon Floor.
  • Use the bloody handkerchief on the machine in the control room to get a code (then you can enter Isolation cells A & B)
  • Examine the box in Isolation Cell B to get the bible and the phone.
  • Use the pen on the blank piece of paper on the desk to get a map (again, not required but convenient)
  • Examine the flower nametag and then go to the courtyard and examine the potted plant. You can use your ability to get rid of the grass, but if you don't want your corrosion rate to raise, just use the sickle you'll find in the top left corner of the courtyard
  • The terza rima puzzle answer is 'fish' 'rose' 'organ' 'star' in that order.
  • Go back to the hidden stairs and call back.You need to find all the rats and read the reports before you do this. You'll know you've read all the reports once you read the last report and get the ROM. If you don't get it when you read the last report, you've missed one. You'll have to find the one you missed and then go back & read the last report again. The last report is in one of the rooms past the hidden stairs, and you'll see the Isolation Cell A rat only after you've finished the terza rima puzzle.
  • Lure the monster to Isolation Cell A, just like Riku suggests. 
The path after that should be relatively simple. 

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