Before you read this, it would be wise to atleast play the game first without the help of anything. This guide contains massive spoilers and would ruin the game on your first playthrough. I am missing a few achievements but this covers most of them. I hope this helps some of you.

I tried to organize this guide in order in which you get these achievements, however given the nature of the game and all the choices you make and the consequences that follow, it isn't exactly right.

You can not get all the achievements in one playthrough, as certain decisions early on in the game prevent you from getting other acheivements later on. You can however use save/load to try and get as many as you can in one playthrough.

Thank you for all those who contributed to the guide, well done!

Anti-Bishop
Kill all attacking Homeless Mercenaries in combat, not including F35s

When Kiril and his men board the ship, kill all of them.

Homeless, But Alive
Incapacitate all attacking Homeless Mercenaries in combat, not including F-35s

(Can be buggy) Same as above but instead you have to incapacitate everyone. I tried doing this when I had Kiril board the ship more "peacefully" and it didn't unlock for me. If it doesn't unlock you may have to have him and his men board the ship in a more hostile manner.

Enemy Mine
Tell Kiril Angelov who you really are

In order to do this you need to get a positive alignment with Kiril when you speak to him in mission ops. Then convince him to let your crew live and only capture you. When the mercenaries board the ship go up to them and DON"T piss them off. Just let them take you to Kiril. Tell Kiril you have something to say and then tell him who you are.

What’s that Smell?
Capture Kiril Angelov through subterfuge

In order to do this you need to get a positive alignment with Kiril when you speak to him in mission ops. Then convince him to let your crew live and only capture you. When the mercenaries board the ship go up to them and DON"T piss them off. Just let them take you to Kiril. Tell Kiril you have something to say to him but not in front of his men. You will go back to the bunker area and the achievement is yours.

Kill Me, Will You?!
Kill Kiril Angelov

When Kiril boards your ship, no matter what scenario happens, kill him.

Mercy for the Merciless
Capture Kiril Angelov through combat

When Kiril boards your ship, whether peacefully or not, don't kill him, instead incapacitate him.

Controlling Dolus
Discover the truth about Bishop Six before you joined with him

In order to get this you need to capture Kiril, at the end of the game when you speak to him, choose the dialogue options related to Bishop six.

It’s Raining Men!
Incapacitate all attacking F-35s

In the sequence in which you have to defend your ship against attacking plans make sure you incapacitate them only and not kill them. Use the left mouse button to incapacitate them. Shooting down missiles is fine.

In the Pie, Five by Five
Destroy all attacking F-35s

In the sequence in which you have to defend your ship against attacking plans make sure you kill them by using your right mouse button.

Hit the Turps
Save Wade from uncertain death

At some point Wade will be in trouble repairing the ship and needs your help (I don't believe it matters whether you complete the sidequest or not) Go into the room, you are then told to leave because its too dangerous. Wait for rook 25 to make adjustments to your suit and then re enter the room and save him and then exit immediately and you will get the achievement

Drink with the Flies
Did not save Wade from uncertain death

At some point Wade will be in trouble repairing the ship and needs your help (I don't believe it matters whether you complete the sidequest or not) Go into the room, you are then told to leave because its too dangerous. Wait for rook 25 to make adjustments to your suit and then re enter the room but don't bother saving him. Just leave the room immediately.

Longer Than Others!
Pawn 64 is doing A-O.K.

Near the end of the game when Pawn 64 asks to speak with you tell him you will meet him in your cabin. When you go to the cabin and the air start running out, if you saved Wade earlier then you will get this achievement

WistleBlower Down

Near the end of the game when Pawn 64 asks to speak with you tell him you will meet him in your cabin. When you go to the cabin and the air start running out, if you did not save Wade then you will get this achievement

Just Call Me Detective
Discover the identity of the traitor

When rook25 asks you who you think killed pawn 7, choose pawn 32

He Chose... Poorly
Never discover who the traitor is

When rook25 asks you who you think killed pawn 7, choose anybody but pawn 32

Now You See Me...
Have the traitor take the easy way out

After you confront the traitor, keep talking to her until she disintegrates herself

Revenge, Cold as Ice
Kill the traitor

When you discover the traitor and confront her...shoot her as soon as you get the chance. Your colleagues won't like it.

Pray Another Day
Capture the traitor

When you discover the traitor and confront her...knock her out using the rifle

Farewell, Steve
Have Steve fall from Zenlil

Farewell, Luca
Have Luca fall from Zenlil

Farewell, Carla
Have Carla fall from Zenlil

If you choose the wrong person for the traitor you will then have to fight him on the ship. Shoot the airlock doors around the ship and hopefully your crew mates will fly out. You need steve, calra and luca to fly out. Just run around the ship blowing open the doors. Reload if you don't get it, some of the crew mates seem to move around.

Wirehead
Completed 21 levels of the Civilian Defence Scenario

Later on in the game you will have access to play a game in the VR in which you defend civilians against robots. After you finish all 21 waves you will get the achievement

But They KEPT TALKING!
Completed 21 levels of the Civilian Defence Scenario and let all V.T. Civilians die

Later on in the game you will have access to play a game in the VR in which you defend civilians against robots. Let all the civilians die and then complete all 21 waves.

You’re So Strong!
Completed 21 levels of the Civilian Defence Scenario and kept all V.T. Civilians alive

Later on in the game you will have access to play a game in the VR in which you defend civilians against robots. You have to keep all civilian robots alive, you can heal them in-between waves. After you finish all 21 waves you get the achievement.

Lost in the Stream
Address the John Wilconson conundrum

Later on in the game you will have access to play a game in the VR in which you defend civilians agains robots. After you finish all 21 waves go to the middle of the map and fall down. You will end up in a white room with a blue robot. Talk to him and then kill him and the achievement is yours.
Another Method- Once you are in quantum limbo after the last jump. Turn around and notice a blue sign. Collect a few of those and you will teleport to a white room with a blue guy. Talk to him and then kill him. Thanks to Mosquito Señorito

Who, Me?
Allow proof of your origin to be discovered

In the beginning of the game when you are question by rook 25 you need to answer strangely so that she recommends you go to the med bay. At the med bay tell them you are from parallel world and keep telling them you are serious.

Bishop 1, Mercs 0
Save the life of Gary Ma

After you are attacked Gary Ma will fall down, go up to him and heal him.

Vague Theories
Tell the Consortium Queen who you really are

In order to get this you have to have told Rook 13 in the medbay who you really are as well so that he can verify your story when you tell the queen.


Soule Music
Is that Jeremy Soule they’re hearing?

Talk to pawn 11 after she finishes her "maintenance" in the brig early in the game. Ask about that
song she was whistling and tell her that it's Jeremy Soule's. Later on, when questioning her and Pawn 44 she will mention that she isn't the only one who hears it. The achievement should unlock.


Cannonball!
Throw yourself off Zenlil

Blow open an airlock door and walk out. Easy achievement

I'll Join your enemies

Negative or neutral alignment from Knight15, interrogate pawn 11 and speak to pawn 64 right after
that. Later on, speak to pawn 64 and convince him to tell everything. After the talk with pawn 64, K15 will ask you to talk in her cabin. Tell her that you won't get along. Thanks to Mosquito Señorito

Enemy in orbit.

Might be not entirely right, - neutral, negative or low alignment from Kirill, Kirill is in the brig. Near the end, talk to Kirill in the brig. When he asks what can Consortium give him, mention his family in Varna. When he asks where exactly in Varna is his family sya that you don't know. Thanks to Mosquito Señorito

It Was A Blonde
Discover what is Farewell, My Lovely

When you interrogate pawn 4 he will mention something about an author in 1940. Ask him about it and then afterwards head over to the bunker area and check his locker.

Nighty Night, Bishop
Fall asleep again
Near the end of the game Knight 15 will tell you if you want to go to VR or back to bed. Go back to your cabin and close the door and use the bed.

Ubezhishte!
Discover a Stowaway aboard Zenlil

From the developer:
You can do this only by Killing Angelov and then continuing to play through the game. It's a major thread deviation and opens up new content toward the end, after dealing with the Traitor

From [Keller]NoVeXX 32:

Trick angelov to board zenlil.
When in hangarbay wait till he boards the ship. as soon as he does, shoot him to death.
Never talk to the two pawns that repair the hole in the hangarbay. Else, talk with everyone. Do the repairs for R15 and have the full conversation with her.
!!! Rescure Wade. !!!!
When Pawn 64 comes to you, tell him he can trust you and hear him out afterwards accuse P32 when asked. After having a conversation with K15, you will be forced to either kill P32 or not. Just render her unconscius after the you mention her husband as suggested with the stungun.
Now ♥♥♥♥ gets interesting. K15 wants to lock up all the pawns and gets in a fight with R15 over the CMC about it. When prompted tell both to stay calm, then side with Alana (Tell K15 she made a few odd decisions).
You're in a bugged part of the game now. Although the whole ship is on attack from the Virus, the Pawns act as if you're still in the interrogation Part. You already caught P32 and Talked to P64. Go back to the Hangarbay and talk to the repaircrew, P11 and i guess 13?. Then Go to the Chessboard and (even if you done so already) repeat the conversation with the chessplaying Pawns. OK we had our fun. Go to B8s old cabin and get the weird unit off the uncontious P32. Equip it. Now take the control chip. The ubezhishte achievement unlocks in the following conversation.

Airlock Fun

Thanks to Gaboris and ResignedFactor

1 You can get it right at the start when you get to enter the cockpit
2 Ask if that was his mother on the line
3 You have to ask Wade about his first love being his ship.
4 Ask if wade needs a girlfriend
5 Agree that Linda is a good name.
6 Call wade creepy.
7 Tell him to watch his mouth next time
8 Joke about how it's a bad idea to ask for coffee.
9 Get surprised that he ACTUALLY threw people out the airlock before.
DONE! He also gives you a keyword to use on the Info Console, but I'm not sure if it works since I tried that before and didn't get anything on it, but maybe it gets "activated" after he talks about it.

Fine, screw you guys!
Have Pawn 4 end up in the Brig

Thanks to Gaboris and ResignedFactor

#1 Talk to Pawn 4 once the investigation starts.
#2 Don't back out and just ask him about the book once the conversation is done.(You don't have to be mean with him.)
#3 Find the book.
#4 ABSORB the book! (Important!)
#5 Go to the one mentioned in the message. (You can also talk to P4 before that, but nothing changes.)
#6 Go along with the conversation. (No mater what you say.)
#7 Wait till the end of the game just before gearing up for the jump.
#8 Go to the barracks and find the one mentioned in the message once again.
#9 Don't back out of the conversation and P4 will just give up and lock himself up.