This guide is aimed for achievement hunters and players that like to 100% games.
Duration to 100%: 50-150hrs (depending on luck mostly)

Learn how to spot them, here is a list of mutation machines:
Good Mender Machine
Gives one endo-mutation













Upgrade Mender Machine
Gives upgrade randomly to existing exo-mutation













Change Mender Machine
Upon hitting corresponding button of the mutation you exchange this exo-mutation for another randomly chosen one.











Broken Mender Machine
Has a chance to get good or bad endo-mutation.














Bummer Machine
Gives bad exo-mutation upon entering pink circle and staying there for certain amount of time.












Here are some most useful tips:

• Use roll a lot - While in rolling animation you are invincible to direct attacks.
  
• Use ranged aim mode - If you have ranged attack mutation be sure to switch to aiming mode with TAB key (default), this mode will make shooting way easier and also for spinning tricks that are needed for finishing tasks.
  
• Remap your mutations - You can remap your mutation buttons when you hold Capslock
  
• Grass and flowers you leave behind - This trail might seem like useless thing, but once you make it, your speed while on grass and flowers is enhanced (about +50% speed boost). Enemies can destroy grass with fire.
  
• Cracked floor or walls - These underground cracked floors or walls can hide secret locations with chest and/or npc
  
• Read tips during loading screen - can be somewhat helpful when you are new to this game

These achievements are unlocked by collecting "logs". You have to find and interact with structures that make you listen to part of the lore. There is no guarantee that you'll find them in every level. They aren't that common.
World 1 lore monuments - Found outside in main world level













World 2 lore monuments - Found inside caves. You'll need Floppy keys for these to access cave.















World 3 lore monuments - Found through triangle portals and then transference gates in sky that leads to some sort of Mender crypts.


(Unlock 25% of the Tome of the Ancients)

(Unlock 50% of the Tome of the Ancients)

(Unlock 75% of the Tome of the Ancients)

(Unlock 100% of the Tome of the Ancients)

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Here are grind achievements, you get points for playing the game and then you automatically unlock weapons, quirks and style just by playing plenty of runs:

(Unlock all styles)

(Unlock all weapons)

(Unlock all Quirks)

(Fully upgrade the town statue)
This achievement unlocks once you successfully finish all endings (8 runs).


To sum this up you can check all your progress in Extra → Tome of the Ancients

Achievements related to currency, in this case these are tapes and CDs:

(Upgrade Shermie's Shop)
Shermie is Townfolk trader located on left of the gate in Homeworld at the beginning. You get this achievements by buying 3 items from her. It doesn't have to be in same run.
(Upgrade Shermie's Shop to the max!)
Same with Cool Customer achievement, keep buying items until this achievement pops up.

(Become a Platinum member)
Everytime you have any currency left after defeating level boss, go though the left gate to your home world. Currency stays in your bank account across all runs. There is a deposit ATM in the town and after you have 100+ tapes on your bank account, this achievement unlocks and you become a Platinum member.

(Become a Desert Chrome member)
Just like with Tapes Never Sleep achievement, except you gonna need to have 5000+ tapes in your account.

(Eject 100 tapes from an ATM)
You can eject 100 tapes in any world once you find one. However it's best to eject the tapes in starting level and then put them back.

Achievements focused on killing normal enemies:

(Annihilate 5 enemies at once)
Get Spikes, Beast Mode or Dungeoness Crab mutation rather, gather 5 or more feeble enemies in world 1 and use your ability to kill them all at once. Personally I think Beast Mode power attack is easier since it all counts as one attack if you hold it.

(Get a Kill Streak of 10 or more)
Once you get to level boss that spawns small enemies, focus on these enemies and pace it so you can have a kill streak until 10, you'll have about 3 seconds between each kill and from kill streak 5 you'll see number indicator rising when you kill an enemy.

(Get a Survivor Streak of 10 or more)
The same as Killer! achievement except you have to be in low health state the whole time. You know when you are in low health state when you hear the audio cue and red edges on screen.

These achievements are Mender Altar related. You exchange items by holding your use item key until you drop the item (default C). There is a chance that Mender Altar will not accept the offering. Note that having Bodacious Endo Mutation will make Mender Altar always accept the offering.

(Receive disapproval from the Mender altar)
Once your offering is not accepted, you get this achievement unlocked, along with the three shots to your butt.

(Receive a cash payout from the Mender altar)
Check the table below to make sure you pick one with the money.


(Receive a tasty beverage from the Mender altar)
Check the table below to make sure you pick one with the beverage.


Here is table of what you trade in exchange:

These achievements require to fulfill tasks given by npcs around different worlds:


(Help Billy farm a plant)
Billy is half goat looking farmer in starting town, he's located on right and down in front of the gate. He will ask you to bring him plants. Bring him Drupe from first world. Hold item button until you drop it near him (Default C).
(Help Billy complete his garden)
Bring him all remaining plants to get this achievement. To be precise you have to first walk over the place to make the hidden fruit grow, manure artefact can help you. Be sure to check your mini-map, fruits are indicated with orange along with other usable items. There are 3 plants in total you can gather: Drupe (starts at World 1), Boom Berry (starts at World 2), and very rare Fruit King (World 3)

Completing first task given by npc in any outside world.(most likely to knock pink cocoon looking sacks from wires)


(Complete Cathode Raider Tasks)
In order to get this achievement, you have to interact with community members located in world 1 and complete these tasks. (You can only complete one per a run)
Here is list of some of these tasks:

• Destroy nests: 2 nests on wires, knock them down.
  
• Perform a 720: Get to somewhere high and jump down while you spin around 3 times. (tip: use TAB and spin with mouse)
  
• Repair antenna: Very close, just go up and get a good whack on it few times.
  
• Help to find a missing person: marked on the map, enter the sub-level to find a missing person, loot the remains and return back.
  
• Extinguish a fire: Jump next to the fire and press slam button (default E).
  
• Light a fire: You gonna need Firearm mutation in order to light it or Boom Berry item.
  
• Find a hatch: Find hatch to a bunker and open it.
  
• Exterminate enemies: Sometimes they ask you to kill all enemies in certain area.

(Complete Transfigured Tasks)
Same just like Honorary Disciple achievement, except this time these tasks are given in World 2 by mutated npcs.

(Complete Vestigial Tasks)
Just like with Honorary Disciple and Commune Contributor, but given by cebernetic/hybrid machines in World 3.

These are achievements that didn't really fit in any other categories:

(Participate in a Daily Challenge)
In main menu, there is option to play Daily Challenge, just click on it. You don't have to finish the run successfully.

(Heal, burn and heal some more using fruit)
Easies way of doing it is to give all 3 fruits to Billy in garden which unlocks another achievement, then after they are all ready to pick up, take the Fruit King, enter level, find Drupe, get damaged, use Drupe, get burned by fire then use Fruit King. I'm not sure if it has to be this order, but it worked for me.

(Discover a Mutation Combo)
Use both mutation buttons while having two mutations that can combine together. Firearm mutation goes nicely with Warhead or Toxic Dump. (tip: get Firearm mutation on beginning with Ranged Exo-Mutation Assist option in Main Menu > Options > Assist Features)

(Complete the game De-Made style)
Successfully finish run with De-Made quirk selected at the beginning. Remember that you don't have to kill most of the enemies and dodging is your best friend. If you are low on health, between each level (in town), buy healing stuff from Shermie, save the game, reload and buy again (Shermie replenishes her wares every time you reload)

(Load your body up with the bummer mutation trifecta)
Find this Bummer Machine with pink circle around it, stay within the circle for a moment and you'll get bummer mutation in exchange for your good exo-mutation. Repeat until you have all 3 bummer mutations.

(Capitalize on your bodaciousness)
Have Bodacious endo-mutation while you walk to traders in Worlds, you'll get free beverage from them and achievement unlocks. Should work same with Mender altars.

(Stay aloft for 10 seconds)
Ideally obtain Wind Bag and Batty mutations, Batty should be enough though. Now find some high spot on map, jump and try cover as much distance and time as you can, while you flap your wings once in a while. Easier done in later levels where there are high and low points on map.

(Pop a chicken with your snake head)
Once you get Cobruh/Snake mutation you can find a chicken after any boss fight before leaving the level for the home world. Gulp it.

(Conceive a serpent baby)
Key to this is to have Cobruh and Death Roe (hatching mutation) at the same time to hatch serpent babies.

(Steal a key from a shop using Suck Face)
As the description says you have to get Suck Face mutation that works like a magnet, then you have to suck a Floppy Disk from traders, for free.

(Defeat the Colossus)
Defeat the final boss.


(Shamefully fall to your death while fighting the Colossus)
While fighting the final boss fall from edge of the level and die. Dying from boss attacks won't unlock this achievement.

This is my first guide so there might be some errors. Let me know in comments if I missed something.