Colony Ship has 70 Steam achievements. Most of them are fairly self explanatory and they'll unlock as you advance the story, but there are a few that are optional and/or less obvious. Unlocking all of them will require either multiple playthroughs or a whole lot of saving and reloading.

This guide goes through all of the achievements and how to unlock them. I've kept the commentary short in most cases, since the goal is more to point you in the right direction rather than provide step by step instructions.

The Sons of Liberty
Support Jonas in the Pit's conflict

The Regulators
Support Braxton in the Pit's conflict

Lord's Mercy
Support Mercy in the Pit's conflict

To support Jonas of Braxton, simply choose one or the other and finish the questline. To leave Mercy in charge, you'll need to

• initially support Braxton
  
• talk Mercy into joining your side
  
• join the frontal assault
  
• accept Mercy's proposition after the fight against Jonas.

Assassin
Assassinate Mercy in stealth mode
Requires you to fail to talk Mercy to your side, then get a quest to infiltrate her fort and kill her in stealth.

Frontal Assault I
End the Pit's conflict frontal assault style
Self-explanatory. There is no equivalent achievement for the non-violent option.

Hidden from the World
Discovered a strange machine
Unlocked when you get into the depot in the Armory.

Survive the Ambush
Stay and fight with Smiles
You'll get ambushed on your way to the Habitat. Stay and fight to unlock.

Requiem for Detroit
Eliminate the Detroit gang
Choose to fight the Detroit gang to unlock. This is one of the hardest fights in the game, since you'll be outnumbered, surrounded and out of cover.

Detroit City
Help the Detroit gang take control of the Toll Road
When you go meet the Detroit gang, side with them instead of Stanton. Requires either diplomacy or combat.

The Black Hand
The Black Hand controls the toll road
You'll first have to take out the Detroit gang, then go talk to the Black Hand leader but don't help the assault by either stealth or speech.

Thy Brother's Keepers
Help Thy Brother's Keepers take control of the Factory
First either talk Bartholomew into siding with the Keepers or kill him and his crew, then help to take out the Black Hand base either through speech, stealth or frontal assault.

Infiltrator
Infiltrate the Black Hand base
Will unlock if you succeed in the stealth mission. You'll need some computer skills as well as stealth skills.

Frontal Assault II
Join the frontal assault on the Black Hand base
Self-explanatory.



The Habitat for Humanity
Reach the Habitat
Unlocks as soon as you are done with the Black Hand base.

Free Bay
Support Moses to keep the Shuttle Bay free

For the Glory of the Mission
Convince Moses to join the Protectors

In the Name of God
Help Nico to take over the Shuttle Bay

You'll gain access to the Shuttle Bay from the Habitat entrance. These are the three possible outcomes for the conflict at the Bay. The Protectors option requires speech skills, other outcomes can be achieved by multiple means.

The Servant of Three Masters
Complete quests for all 3 factions in the Habitat
That's the Brotherhood, the Church and the Protectors. You'll have to approach at least one to advance the main quest; if you do work for all three, you'll unlock this achievement.

Per Aspera Ad Astra!
Offer the machine to the Church

For Liberty and Justice!
Offer the machine to the Brotherhood

The Mission Above All!
Offer the machine to the Protectors

Gain access to the faction leader and select the dialogue option to offer the machine to them. "Per aspera ad astra" means "through hardships to the stars", by the way.

The House of Ecclesiastes
Talk to Ava
You'll gain access to the ECLSS after having offered the machine to one of the factions. Talk to Ava to finish the second chapter.

The Matriarch
Make a deal with the Great Mother
Requires speech skills.

The First Daughter
Help the First Daughter to ascend
This is the violent option for acquiring fuel for the machine.

Fungicide
Clear Hydrophonics
Stop the ongoing experiments (and thereby clear the toxic air) in the yellow and red zones to unlock. The critters in your way can be dealt with by either stealth or combat. They're not really open to diplomacy, though.

Frontal Assault III
Attack the rival faction at the Armory
Near the end of Chapter III a rival Habitat faction will show up at the armory to demand control of the machine. Fight them to unlock. This can be a difficult fight.

Terminated
Kill Azrael
Three monks will ambush you when you are delivering the machine to the Habitat if you are taking it to any of the Habitat factions. Fight and kill the monks to unlock.

Sealed & Delivered: Church
Deliver the machine to the Church

Sealed & Delivered: Brotherhood
Deliver the machine to the Brotherhood

Sealed & Delivered: Protectors
Deliver the machine to the Brotherhood

Each of these will require you to get through Azrael and his buddies (see above).

Sealed & Delivered: ECLSS
Deliver the machine to the 'monks'
If you are siding with the monks and killed Mathias earlier, you'll have to fight a Church ambush. Otherwise you won't have to fight anyone during delivery.

Kingmaker
Complete the final faction quest in the Habitat
This is probably the most convoluted achievement to unlock, so I'm going to go ahead and copy what skaudus wrote in the discussions:

Originally posted by skaudus:

In the Habitat, Chapter 2:
1. Save the Brotherhood Spy.
2. Tell Silas (Protectors' leader) about him. He'll send you to talk to Hanson (Brotherhood Leader)
3. Hanson will ask you to first deal with a traitor in his inner circle. When you return to the Protectors' area, Sheffield (Chief of the Secret Police) will talk to you. You need to convince him to reveal the traitor's name.

4. Now things can branch out a bit.

a. You offered the Machine to either the Protectors or the Brotherhood:
i. Deal with Eden by convincing her to come back into the fold or kill her
ii. Talk to Hanson and then to Silas about it.
iii. Keep playing the main quest.

b. You offered the Machine to the Church:
i. Talk to Abraham and get ready to plant some evidence.
ii. Talk to Eden and let her in on the Church's plan.
iii. Talk to Hanson.

5. After you successfully deliver the Machine to one of the Habitat factions (so *not* the Monks), you'll get a prompt to go talk to or kill Sheffield. Completing the quest earns you the achievement.

Offer they can't refuse (Brotherhood)
Help the Brotherhood annex the Pit

Offer they can't refuse (Church)
Help the Church annex the Pit

Offer they can't refuse (Protectors)
Help the Protectors annex the Pit

Deliver the machine to one of the three Habitat factions (not the monks), then talk whoever is in charge of the Pit into agreeing to annexation.

By Other Means
War is the continuation of policy by other means
Deliver the machine to one of the three Habitat factions (not the monks), then fail to annex the Pit for them.

Freetown
Help Jonas keep the Pit free

• Side with Jonas in Chapter I
  
• Form an alliance with Moses in Shuttle Bay (to do this, first choose the Persuasion option to accept Rowley's offer, then suggest allying with Jonas instead)
  
• Deliver the machine to one of the three Habitat factions (not the monks)
  
• Make sure your reputation with the faction is at 20 or more
  
• When sent to annex the Pit, appeal to your faction rep to keep the Pit free.

The Driver's Seat
Reach the Bridge
Unlocks near the end of the main quest line. You'll need to get past a robot, which can be done in multiple ways.



The Way of the Forefathers
The Ship remains in orbit while the Protectors take over

The Dream of Liberty
The Ship remains in orbit while the Brotherhood takes over

Kingdom of God
The Ship remains in orbit while the Church takes over

Deliver the machine to one of the three Habitat factions, reach the bridge, and return to the faction leader to deliver the news.

The Pilgrims of Terra
The Ship remains in orbit while the Monks assume control
As above, except you'll have to go talk to the Habitat factions. Doesn't change much if you fail the speech checks, you'll get the same ending anyways.

I'm Outta Here
Take the lander
After reaching the bridge, return to the the lowest level of Mission Control and use the lander. Requires high level computer skills.

Return to Sender
Send the Ship back to Earth
Decide against landing once you reach the bridge. There is a very difficult fight against Ava and her guards at the end.

The Promised Land
Initiate the landing sequence
After reaching the bridge, return to the Heart and convince the Great Mother to turn off the engines. Then return to the bridge, kill the monk guards and initiate landing. Can only be done if you killed the old Great Mother in Chapter III.

True Hero
Complete the game on Hero difficulty mode

Always Bet on the Underdog
Complete the game on Underdog difficulty mode

True Hero will also unlock if you finish the game on the harder difficulty mode.

Fix the Bioreactor
Help the Grangers fix the bioreactor
Head to Hydroponics in Chapter I and help out the Grangers.

Reporting for Duty
Repair the riot control robot
It's in Mission Control. You'll need to gather some parts in various areas of Mission Control.

Versus Machine
Kill the combat robot for Eli
In the maintenance tunnels, in Chapter II or later.

The Eye of the Synod
Steal the mummified eye from the Church's tomb
Also in the maintenance tunnels. You'll need a character very skilled in sneaking, relying on gadgets alone is not going to cut it.

The Harbringer
Recruit the Harbringer
Finish the fights at the Pit's courthouse in Chapter I and Harbringer will come talk to you. Find Knurl in Mission Control during Chapter III and kill him - note that Jed will side with Knurl so don't bring him with. Then head to the Heart and after some dialogue Harbringer will get recruited.

Mutant
Get a mutagen injection
Kill a psyker frog and harvest the brain, then kill three more and harvest the brains. Maryam, the lady at the cultivation lab in Hydroponics, can use the brains to make you an injection.

Urban Pacification
Deploy Romeo in Combat
There are several options to deploy Romeo in combat after you put it together: in Mission Control, in the Armory, and during the machine delivery trip. It needs to be powered up first, though.

Ol' Bub
Kill Ol' Bub in its lair
In Mission Control. A fairly difficult fight, you'll pretty much need energy weapons for this one.

Bounty Hunter
Collect all bounties in the Habitat
A lady at the Protectors admin district will offer you three bounties. To unlock the achievement, take on each fight and return for your rewards.

Ace Prosecutor
Win every case in the Courthouse
Win a few fights of increasing difficulty in chapters I and III, respectively.

Curiouser and Curiouser
Discovered a lander
It's at the lowest level of Mission control.

Augmented
Install an implant
Can be done very early on at the Pit.

Overclocked
Overclock one of your implants
Eli at the Maintenance tunnels will offer overclocking services once you get there in Chapter II.

Barely Human
Install all seven implants
You'll need the Healing Factor heroic feat or you won't be able to install all seven. The subliminal implant can be a bit hard to find, but there are several available in the game.

Pure Human
Complete the game without installing any implants
Easiest to unlock as a pacifist build.

Negotiator I
Complete Chapter I without fighting anyone

Negotiator II
Complete Chapter II without fighting anyone

Negotiator III
Complete Chapter III without fighting anyone

Master Negotiator
Complete the game without fighting anyone

Requires a character with advanced speech skills ... and nothing more. Easiest way to finish the game.

Stealth takedowns don't count as "fighting", as far as these achievements are concerned.

Deadly
Earn a combat reputation of Deadly

Mentally Unstable
Earn a combat reputation of Unstable

Murderous Psychopath
Earn a combat reputation of Psychopath

"Psychopath" is the highest level of combat reputation. There are more fighting opportunities available than are needed for this achievement so you don't have to kill just everything you come across. It does take a whole lot of fighting, though.

Killed in Action
Lost a party member in combat
Getting knocked out isn't enough, they have to be permanently dead.