This is just a quick guide detailing the requirements of every achievement, which covers pretty much every secret and ending in the game except for the boss rush. If you want more details on how to find the secrets I'd recommend checking out these guides :

https://cs2bus.com/sharedfiles/filedetails/?id=815227072
https://cs2bus.com/sharedfiles/filedetails/?id=455408513

These achievements are unlocked after defeating their respective boss.


If you beat the game you should have encountered all these bosses already.

Class C
Defeat the Class C Guardian


Carapace
Defeat the Queen Beetle


Garbage Collection
Defeat the Scrapping Unit


Sea Monster
Defeat Serpent 5


Plant and Blood
Defeat the Overgrowth


Trio
Defeat the Class D Guardians


Scitterer
Defeat the Tomb Spider


Stony Gaze
Defeat the Robed Statue


Festering Matter
Defeat the Plague Hive


Access
Defeat the Station AI


Firewall
Defeat the Security Overmind


Class A
Defeat the Class A Guardian


Recycler
Defeat the final boss




Regulator
Defeat Multicore


Invincible
Defeat the Mending Unit


Pillars
Defeat a boss
This achievement is for defeating Mwya first form


Haunted
Defeat the Restless Spirit


Eyes
Defeat a boss
This one is for defeating Mwya 2nd form, which is accessible after defeating it's first form.

These achievements are for beating the different endings of the game.


Environmental Station Alpha
Beat the game
Get the first ending by beating the Virus


Abandoned
Reach an ending
Get the 2nd ending by going right when you get to the planet surface (so right of Mwya first form).


New Role
Reach an ending
Get the 3rd ending, by killing the ghost, and going right after finishing the maze.


Whoops
Get hit by a meteor
Get the regular ending by beating the Virus on New Game+


Forced Destiny
Reach an ending
After beating Mwya 2nd form, you can return to your ship and try to leave the station to get this ending.

Full Course
Beat the game with 100% completion


Fuller Course
Beat the game with 200% completion


To reach 200% you need to beat every bosses, get every secret, but also trigger every story flag in both normal and New Game+. Since you start with every power-up in New Game+ it can be pretty easy to miss some story flag. Make sure you :

-Get level 2 access at the beginning of the game
-Turn on the Diskette reader
-Turn on the Overgrown module
-Turn on the generator near the Class D Guardians
-Destroy the orbs in the temple
-Destroy the monitor in "The Reference" (to the right of the second elevator shaft)
-Activate all Pillars and get every Key (thankfully the Eyes are still open)
-You also get 1% for both the Virus and Planet endings

The maximum you can get is 203%. For some reason it seems right now you can only trigger this achievement by getting the 2nd ending, where you go on the planet.

▓▓▓
███
Go right of the clockroom with anything other than 1 power-up activated.


Owch!!
Those things are sharp!!!
Die to orange spike, in the room below the golden teleporter that transport you to the planet.


Data Storage
Find every diskette


Ever Deeper
Take a step
Find one of the 4 keys.


Watcher
Open an eye


For these three achievements, see this guide for more info
https://cs2bus.com/sharedfiles/filedetails/?id=455408513


Coolest Robot
Find a hidden treasure


Get the bicycle. It's found on the derelict ship 30-21, you can access it by using the booster X to go in the pipe in 30-20.




F R I E N D S H I P
Find a hidden treasure


This final secret has a few steps to it in order to find it, which you can find in the comments of the guide I linked above.
To get the achievement you only need to do the last step. You need to enter the secret room in 15-09, which is the secret room where you find the key where you have to wait a few seconds to open it. Go down one square (but not in the room where the key is) and type "CROWN" in front of the left wall to open it.

Rushing
Beat the game in 1 hour


This achievement is not that bad, since the game will only add the time you spent alive, so you're allowed to die as many time as you want. As long as you follow a good route, you should be able to get it.
Two very good speedrunning trick that don't require a lot of skill to pull off are :

Booster V skip
You can get the Booster V upgrade as soon as you get the double jump upgrade. It relies on the fact that when you take damage, your character will go up vertically. For more info I advise you to watch the timecode of this video.
https://youtu.be/Z85j1wqik5o?t=326

You can use your hookshot in the room to the right of the final boss. Letting you skip the entire Guardian A section.
https://youtu.be/Dh59Vu1TOwc?t=4293

If you use these two skips and don't waste too much time, you should be able to get the speedrun achievement pretty easely.

Thought you could escape?
Get outrun by a ghost


This is the only missable achievement in the game. To get it you need to board your ship while the ghost is chasing you. It can be either the Virus ending or the ending you unlock after defeating Mwya 2nd form.
The ghost does not respawn in New Game+, so if you killed it before getting the achievement, you'll have to redo everything again.