These achiviements are awarded by simply progressing through the main story. Most of them cannot be missed.

Rigged And Ready
Acquired an Exo-Rig
Activate the first Medbay in the game.

Jailbreak
Defeated Warden Garcia
Sever his right arm to get the MG Jackknife Pro.

Overheated
Defeated Little Johnny
Sever both his little claw hands in front to get the Little Johnny's Forceps V2.0.

Studied The Blade
Defeated Captain Cervantes
Sever his left leg to get the Jag-1000 'Carnivore' Shotgun drone module; or sever his right arm to get the JAG-22 ‘Aeterna’ weapon. I recommend getting the drone module since the weapon can be obtained by cutting off an A.I.D. Ronin's arm later in the game.

Home Invasion
Defeated Delver
Break the armor on each of its limbs (arms and legs) at least once to get the Helix of the Delver V2.0.

Luminary
Met Guttenberg
Go to the CREO Institute to collect your reward after killing Delver.

Unforeseeable Consequences
Discovered the Utopia rocket crash site
Awarded automatically on the way to General Shields' bossfight.

Court Martial
Defeated Major General Ezra Shields
Destroy his mech's flamethrower during Phase 2 to get the VULC-88 'Panthera' Rotary Gun drone module. Destroy both of mech's armored legs during Phase 1 and sever his right hand during Phase 2 to get the General's A.C.U. V2.0.

Dead Again
Defeated Brother Eli twice
Awarded after defeating Eli inside the CREO Institute after the world shifts.

Mommy Dearest
Defeated Matriarch Celeste
Cut off both her mechanical arms during Phase 2 to get the Icon of the Spark V2.0.

What A Catchy Song
Activated the Ops Center in the CREO Institute of Technology
Activate the Medbay in the plane hangar of the CREO Institute while following Eli after defeating Matriarch Celeste.

Bad Dog
Defeated H.A.R.O.L.D
Sever the tail to get the H.A.R.O.L.D.'s Holographic Tailblade.

Corrupted Beauty
Defeated Goddess Helena
Sever her right arm to get the Twinlance of Corruption.

Denying Prophecy
Defeated Archangel Eli
Archangel Eli is the last boss of the game; the game goes into NG+ automatically once you defeat him. Destroy each of his armored body parts to get the Greatblade of the Archangel V2.0.

Reborn
Be purified by Athena, cleansed of all imperfections.
Choose to spare Eli after the final boss battle.

Hello Darkness My Old Friend
Be transformed by Athena into a dark avenger, ready to reshape the world.
Choose to kill Eli after the final boss battle.

Both ending achievements can be obtained in one playthrough by reverting the save to the last Medbay. Defeat Eli, make a choice, and get the first ending; after the credits roll, choose continue from the main menu but don't reload your save just yet, select the save and press Y to revert the save to the last Medbay. Defeat Eli again and choose a different ending.

A Little Banged Up
Survived the plane crash in NG+
After the ending, continue your save to go into the NG+ and play through the plane cutscene.

Clean Cut
Cut an enemy's limb with the follow-up to a backstab kick
Sneak up behind an enemy and target one of their limbs, attack them then you see the backstab icon (red circle), and then attack again immediately after that to cut one of their limbs. Easy to obtain with weak enemies inside the Detention Center.

Counter-Sniper
Killed all enemies operating sniper turrets
There are five non-respawning enemies like that in the game. Three of them are in Jericho City Downtown, they are missable and need to be killed before Major General Shields fight if you want the achievement.

• One is in Welder's Block Rooftops just outside the Seaside Court; you can reach them via Central Plaza after the A.I.D. gate.
  
• One is on a building near the entrance to Babylon Gardens; take the second lift inside Cloud 9 to reach them.
  
• One is inside the dark ruined building on the way to Gateway Bravo.
  
• Two last snipers are in Cathedral of the Spark. Take the exo-line near the entrance to reah the first sniper; from the first sniper's location you can easily target the second sniper with your drone.

HEADSHOT!
Kill an enemy with a headshot
Target an enemy's head and shoot it with your drone until the enemy dies.

High Performance
Receive a special reward from a boss
Refer to the section above for the list of bosses and the special rewards they give. Can be obtained early after Warden Garcia boss fight if you sever his right hand.

Offensive Defense
Perform 30 directional blocks
Self-explanatory.

Remote Surgery
Cut off each limb of a humanoid enemy using your drone
You need to sever an enemy's head, body, and each of arms and legs for that achievement. Equip you drone with R-1 ‘Diode’ Laspistol, find a weak enemy, target their limb, and shot it with the drone until the limb is cut off. Repeat for every limb. You can also attack the enemy with your weapon first to weaken them and save ammo, just make sure your drone gets the final shot to cut the limb off. Easy to obtain with weak enemies inside the Detention Center.

Reverse Engineering
Kill a Gideon's Rock statue with its own weapon
This achievement is less straightforward than it seems. I killed the statues with Gaia Lancer many times but the only way I got it to unlock was the following:

• Start the fight with any weapon other than Gaia Lancer equipped
  
• Target the statue's right arm and cut it off
  
• Pick up the scrap that appears
  
• Switch to your Gaia Lancer and finish the statue off

Note that this achievement is missable: it cannot be obtained once the world shifts and all statues in the park get infected with nanites.

Risk Tolerant
Kill a boss while carrying 30,000 Tech Scrap


Shocking
Use the EMP-44 'Starfish' on an enemy
The EMP-44 'Starfish' is obtained after killing Little Johnny.

Sleeping With The Fishes
Drown an enemy in deep water
Can be obtained early by pushing an enemy off the bridge in JCPD district. Very easy to obtain in Port Nixon.

Sorry, Didn't See You There
Kill a cloaked Hunter
Cloaked hunters are in Gideon’s Rock area. Weaken a hunter while they're visible, wait for them to cloak, then deal the final blow immediately.

Triplets
Defeat all Delver Echoes
You will be able to fight Delver Echoes after defeating Major General Ezra Shields. The Echos are stronger version of Delver, but each of them has only one phase. All fights are available until you defeat the final boss.

• Delver Echo Alpha is near the entrance to the CREO Institute from the underground pit you end up in after the Major General bossfight. To start the fight, approach the buried chest in the middle of the arena. Note that you can skip touching the chest if you have trouble with this boss early on and come back after you get better gear.
  
• Delver Echo Beta is in the same location as Alpha; rest at a Medbay after defeating the previous boss and come back for another fight.
  
• Delver Echo Gamma is in a courtyard in Central Plaza where the zebra mural is.

Own Medicine
Kill a Delver Echo with the Helix of the Delver or Helix of the Delver V2.0
You get the Helix of the Delver for defeating Delver in Gideon's Rock. You need to finish one of Delver Echos listed above with the Helix to get the achievement; I recommend Gamma because it's the slowest of the three.

Three Birds With One Stone
Kill 3 enemies at once using the homing missile
To get the achievement you need to obtain a SSM 'Vanguard' Missile first:

• You can get one from Hawke after killing Delver if you meet him in Seaside Court and agree to give him 5,000 scrap.
  
• You can buy it from Rex for 30,000 scrap after rescuing him in the Cathedral. First you need to complete April's Fool (get the plastic rose behind him in Seaside Court, agree to help, find the April's Fate audiolog in a small locked room just before the boss arena in Port Nixon, return to Rex and tell him the truth about April). After the world shift you can find Rex locked inside the Cathedral of the Spark; find April in the Cathedral and ask her name, mention the plastic rose and she'll give you the key. Return to Rex and free him to get the access to his merchant inventory, including the SSM 'Vanguard' Missile; you can buy it right after rescuing him or find him at Gateway Bravo later.
  
• One can be found in a chest in a tunnel leading from Eli's path to Port Nixon.
  
• One can be found in a chest after compleing the Kraken DLC.

After obtaining the missile, equip it and find a group of weak enemies to shoot, the easiest might be the small nanites near the first Delver arena in Gideon's Rock.
If you want to keep the missile, you can revert your save to the last Medbay after getting the achivement.

Following In Their Footsteps
Collect 10 Strange Visions
Strange Visions are audiologs you can receive after approaching a nanite storm and watching its echo to the end. Most of them are obtained before Ezra Shields fight, with the exception on Strange Vision 5/10 that's only available after the world shiifts.

• Strange Vision 3/10: on a partially destroyed bridge on the way to the Seaside Court.
  
• Strange Vision 1/10: in Port Nixon on the shoreline, near the plane wreck.
  
• Strange Vision 2/10: appears immediately after you kill Brother Eli for the first time.
  
• Strange Vision 4/10: in the couryard in Central Plaza after the first A.I.D. security gate.
  
• Strange Vision 7/10: in Gideon's Rock near the entrance to the CREO Institute.
  
• Strange Vision 6/10: appears immediately after you kill Delver.
  
• Strange Vision 8/10: in the observation room inside the hospital in the A.I.D. Command.
  
• Strange Vision 9/10: on the way to Ezra Shields fight, right past the door marked as "point of no return".
  
• Strange Vision 10/10: on the way to Ezra Shields after the previous Strange Vision.
  
• Strange Vision 5/10: In the Underground after the world shift, above the pit where you end up after defeating Ezra Shields. It's hidden behind a barrier and is easy accessible after you get the Charged Nano Absorption ability and defeat H.A.R.O.L.D.

Stimulating The Local Economy
Spend 50,000 tech scrap at vendors


Can't Trust Banks
Carry 100,000 Techscrap


Powered Up
Reach Core Power 50


Suited and Booted
Equip a full gear set


Full Arsenal
Collect 50 weapons
There is a lot of weapons in the game so this is pretty easy to get, just keep cutting off right arms of the enemies in each new area you go to.

Gotta Craft 'em All
Craft 20 Gear Sets
The set has to be complete and crafted for it to count towards that achievement (head, torso, two arm, and two leg pieces).

Marked For Success
Upgrade a weapon to maximum level
The maximum weapon level is Mk. X. Make sure to upgrade at least one weapon before going into NG+ since maximum for NG+ is Mk. XX.

Defense in Depth
Upgrade all gear pieces in a set to maximum level
Upgrade a full armor set (head, torso, two arm, and two leg pieces) to Mk. X level.

Swiss Army Drone
Acquire all combat drone modules
Note some drone modules are missable. Consumables don't count.

• A.I.D. 'Empire' Sniper Rifle: cut off one of A.I.D. soldiers right arm. (Any of those who shoot at you. You can use your drone to do it at a distance.)
  
• CREO Industrial Magnet: purchased from Rex for 10,000 scrap in the Seaside Court.
  
• GAIA Laser: sever the head of a GAIA Statue in Gideon's Rock. The head might be easier to reach if you cut off one of its legs first.
  
• EMP-44 'Starfish': unmissable. Obtained after killing Little Johnny.
  
• JAG Bio-Sensor: missable. To the left of the first A.I.D. gate is an alley, go there to meet a shady Russian doctor. Accept his quest; go through the A.I.D. checkpoint, take the lift on the right to get to the courtyard with a zebra mural and one of nanite echos. Pick up the drone part there and bring it back to the doctor. Very important: when giving back the part, choose to wish him good luck and do not tell him he is insane so he'll give you the module. (You can revert the save to the last Medbay if you accidentally chose the wrong answer.)
  
• Jag-1000 'Carnivore' Shotgun: missable. Cut off Captain Cervantes' left leg.
  
• Klokonov R-47 Autorifle: cut off an arm of a VULTR scavenger that shoots at you in Downtown Jericho.
  
• R-1 ‘Diode’ Laspistol: unmissable.
  
• S&R Drone: unmissable.
  
• W-102 Banner: in JCPD district on some walkways above.
  
• W-101 Spray Can: near the entrance to the Underground below the broken bridge on the way to the Seaside Court.
  
• SPARK 'Enlightener' Electro-Beam: cut off a SPARK Galvanizer's arm in the Cathedral of the Spark.
  
• VULC-88 'Panthera' Rotary Gun: missable. Destroy the mech's flamethrower during Phase 2 of Ezra Shields fight.

Don't I Know You...?
Helped Benjamin Burke
Benjamin Burke is inside one of the cells in the Detention Center, he calls out to you and asks to help him. Return to open the door for him after you get your exo-rig.

Geronimo!
Fell into the Underground
After you kill Ezra Shields, a hole appears in Downtown Jericho near the building where the Russian doctor is. Simply jump into the hole to get to the underground; wait for the game to load and the achievement will pop.

It's a Trap
Disable an A.I.D. checkpoint scanner gate without triggering its alarm.
There are two A.I.D. scanner gates in Downtown Jericho and two in A.I.D. Command. You'll need the EMP-44 'Starfish' to disable them. Disable at least a gate without passing through it directly or alerting enemies guarding it to get the achievement.

• The first gate is on the way to Central Plaza from All Saints Boulevard. You can sneak up to the magnetic lock in the back by turning into the alley where the shady doctor is and going through the hole in a wall on the right and going up.
  
• The second gate is on the way to from Central Plaza to Gateway Bravo. You can sneak up to its lock by taking the second elevator in CLoud 9 bar and going above the gate.

Note this achievement is missable: once you trigger a gate's alarm at least once in a playthrough, the achievement will not unlock even if you come back later and disable the gate without triggering the alarm again.
There is also an A.I.D. gate you can disable in a pit you end up in after Ezra Shields boss fight but I don't know if it works for the achievement.

It Lives! It Sniffs! It Conquers!
Equip the IRONMAUS set and the Justice of the Iron Maus weapon.
You can get the set and weapon by completing The Incredible Iron Maus.

• After killing Ezra Shields, meet Kyle Baxter at Cloud 9 Bar and agree to meet him at the Catherdral.
  
• Find Kyle Baxter in a small room inside the Cathedral, speak to him and tell him to go out.
  
• Progress through the Cathedral until you find a body with Iron Maus' mark nearby. Then go back to the small room and talk to Kyle again.
  
• Tell him he's injured and send him home.
  
• Find him inside the comic shop at Port Nixon. He will give you the IRONMAUS armor set and his gloves.
  
• Equip the armor set and the weapon, and the achievement should pop.

True Survivor
Met Warren
You first meet Warren near the Medbay outside the JCPD.
After you defeat Little Johnny, come back to All Saints Boulevard, go under the ruined bridge and use the EMP-44 'Starfish' to get into the Underground and meet Warren there. Give him an A.I.D. armor set when he asks (the A.I.D. Nightfall is the easiest to obtain at this point) and proceed through the game normally. You will meet Warren again in the A.I.D. Command near where you get the Force Hook and get the achievement.

Where It All Began
Revisited the Detention Center
Return to the Detention Center after the world shifts. You can use the exo-line in Warren's hideout under the bridge to get there.

You can access the Kraken DLC content after killing Brother Eli for the second time and getting the Lifter Hook. Go to the waterfront in Port Nixon near the plane wreck where you found a Strange Vision before; there will be a boat you can take to access VBS Krakow (the DLC area).

Turbo Booster
Completed plan B in the drive-in theater8
Story-related and unmissable.

Squid Pro Quo
Defeated CAIN - Core Protector
CAIN is the final boss of the DLC. Destroy the drone on his left arm to get the Parrobotic Drone. Sever all his legs to get the Ungula Universalis.

Juiced Up
Completed Proto's Sidequest
Complete The Outsider:

• Find Proto in one of the tunnels and get his power core from him.
  
• Take the power core to the maintenace area outside the drive-in and charge it.
  
• Return to Proto's hideout near the maintenance tunnel behind one of the corners of the drive-in.

Box Office Smash
Entertained Proto by completing 25 enemy waves (up to his second break offer)
After you complete Proto's quest and progress through the main DLC quest enough, you'll get a message Proto is waiting for you at the movie theater. Talk to him and offer to teach some combat moves. Fight through waves of enemies he sends. Once he asks you if you need a break for the first time. Talk to him and tell him you want to continue, then continue fighting until you get the achievement.
It's very easy to get the Can't Trust Banks achievement during this fight if you haven't gotten it already.

Homewrecker
Completed Norm's Sidequest
Complete Breaking The Norm:

• Talk to Norm near the Medbay. Ask him about BBQ.
  
• Get the Frankfurters from the vending machine inside the convenience store and bring them to Norm.
  
• Find the Captain's Luggage by jumping to a lifeboat tied to one of the sides of VBS Krakow and bring it to Norm.
  
• Complete Proto's quest to get the Black Box and bring it to Norm.
  
• After completing the plan B in the drive-in, go up and find a small tunnel near the console, take the magnetic lift, and find the Strange Memory Chip inside. Bring it to Norm to complete the quest.

You can use the key Norm gives you for completing the quest to drain the pool before CAIN bossfight to get an additional drop after the fight: the Red Hot Poker wapon.

Shrimp Cocktail
Killed 30 robotic crabs (any type)
Red and blue robotic crabs are all around the area, plus CAIN keeps summoning them when he sees you. Just kill thirty of them.

Going Postal
Destroyed all mailboxes
There are seven non-respawning mailboxes in the area: six on Cherry Lane and one in front of the drive-in.

Plank of Wood
Pushed the pirate attacker from the plank
When you enter the backyard, you will see a pirate pushing a person off the plank. Run to the pirate and hit them a few times until he falls off the plank (or use the shotgun drone module to push him off).
The achievement isn't missable since the pirate respawns even if you fail to push off him during the first encounter. If the pirate doesn't respawn, you might need to progress with the main DLC quest further before returning to the backyard.

The Easy Way Out
Used the plank to jump off the ship
Jump off the same plank you pushed the pirate off for the previous achievement.

Loot, Pillage & Craft
Crafted all gear sets of the Kraken DLC
The DLC has only two armor sets: COLLECTIVE (obtained by severing the limbs of smaller humanoid robots) and CORSAIR (obtained by severing the limbs of large humanoid robots). Craft a full set of both (head, torso, two arm, and two leg pieces) to get the achievement.