Roughly from memory the steps to beat the game are. (note that you should explore, interact with things unless specified and open any green or red cabinets you find for resources. Also interact with any gleams on the floor for keys that let you open these cabinets, reds have ammo, greens have food. Food is a huge time limit, avoid making unnecessary trips though food is relatively lenient especially if you are opening green cabinets.)
1. Inspect your cell, go to sleep, save your game.
2. Leave your cell, examine the cell with the bed and kill the worms that pops out. Take the key.
3. Explore further, grab the metal bar (better melee than kicking), examine the cell with the infested girl and kill the worms, grab that key.
4. Leave by going back to the left (save at your bed), then go through the door closest to your cell.
5. Go through the hallways until you trigger cutscene where your character runs to the docks. Go all the way back, past the dog and enter the security room at the bottom of the hallway where the cutscene started. Open the key shelf and take the key.
6. Go Back to your bed (save your game) then go all the way to the right and open the red doors. Explore until you find the room with the laptop. Use the laptop to call for help then run from the burly man and enter the locker room two doors left. Hide in the top lockers and wait until he smashes the third locker and leave through the door (he will not follow you). Move the tables and flee past the closing doors.
7. (save your game at your bedroom cell) Go back to the hallway that leads to the docks (where the cutscene occured) and go up the stairs. Follow the left pathway (do not attempt to use any elevators, stay away from them) until you see a double doors in the middle of a hallway. This the main security room where you meet the nice man who helps you. Talk to the man and use the computer room near him to open the doors that closed during the finale of the burly man chase.
8. Go to the left of the main security room and access the doors in the next hallway. The closest one should be the left building save room. (save your game)
9. Go to the left and down the stairs. Go to the right until you see a foyer. Go down the stairs and into the closest door to the stairs. You should find a locker room with ammo in it. You can't pick up the ammo because the dumb bitch you are playing doesn't know how guns work and isn't a kleptomaniac (two things that prevent survival in horror games)
10. Inspect the locker twice until you get a pop up of a gun. Go back to the main security room and talk to the nice man. He will teach you how to use the gun. Be very careful with any interactions with nice man form now on because if you accidentally shoot him, he will go full auto on your ass and kill you in a cutscene. (save your game). From here you can explore to get more ammo. Also be sure to go through the security room to the left of the reception desk and then through to the other side of the reception desk to pick up the key that's by the laptop. Why the MC can't reach across the desk or climb over.... IDK
11. Go back to the laptop room where you started the burly man chase. Inside the hole will be plot coupons, food and other good stuff. It also has keycards you need to advance the game.
12. Go back to the foyer in the leftside building (close to where you got your handgun) go through the double doors and continue past until you meet dark elevators. Assuming I haven't fucked up, you should be able to go through these elevators and enter the laboratories. Go left through the laboratories and down (there is a save room near the elevators and a green cabinet). If you find a room with eggs avoid going in it as you will fight a difficult boss that is likely to kill you. You should eventually enter a series of long corridors that lead to a specimen containment unit (this will trigger a cutscene where the MC tries to access the unit where the captive girl is being held). Keep going to the left and you will fight a small gauntlet of worms (focus on shooting the big worms, don't try too hard to conserve ammo, if you get grabbed, you are probably going to get grabbed again... basically game over if that happens).
13. After the gauntlet, go left and pick up all the stuff. You should get stuck at a mystery door that requires an AT-X card. Pick up the keycard that's in that room.
14. Go back to the foyer in the leftside building (you should get a cutscene about infected scientists dropping infector nematodes, try your best to not get any awful debuffs). Also consider saving your game at the labatory save rooms
15. Go to the right of the foyer in the leftside building to end up a connecting corridor that has a locked gate. Assuming I haven't fucked up the steps, you should be able to open this gate. Go through the gate and through the fields (there will be dogs).
16. You should bump into an aircontrol tower with a save room in the bottom and a radio station at the top (save your game). Pick up the lvl 3 keycard here that's in the aircontrol tower.
17. Now technically I believe you are supposed to go through with the next few steps without doing this part (the game hints you are supposed to do this when you get later steps as the nice man will be injured and will probably hint about it before finally giving you a lesser ending where he GTFOs on a boat) BUT SINCE YOU are already here... Go up from the aircontrol tower and you should meet a curved hill. In the center of the curved hill on the leftside should be a section that will let your MC pass through if you keep running through it. Go through the clearing (ignore the enemies as they are weak if possible), and go down the hill and pick up the key to the radio station. You can also go all the way through into the caves to preview the boat, but do not approach the boat or you will incur megumin's wrath. Go back to the air control tower, stick the key into the machine at the ground floor then head up to the top and use the microphone. If you wish to trigger a newgame plus, head up from the aircontrol tower and go right to the helipad.
18. Assuming you didn't want a new-game plus (or are playing from one), go back to the laboratory and open cell of the captive girl (code is her birthday 0625). The result cutscene should start the next phase of the game. Go back to the security room with the nice man and pick up the key that showed up when he somehow failed to notice bugs sneaking into his room. (save your game).
BONUS: Go to the top floor of the right side building and approach the open elevator shaft. Win the resulting boss fight by shooting the boss repeatedly. You can mash C to give yourself some more time. Try to avoid shooting his minions that grab onto you to drag you closer to the boss's mouth. This will net you access to the elevators (which can quickly take you to the laboratory with your lvl 3 access card and also nets you the magnum)
19. Go back to the laboratory areas and go up. This will take to you the upper area of the laboratories with a hallway that will contain a bottom path, a double doored room and an upper path. If you are on the track to a lesser ending the nice man will be pretending to be injured in the room. If you have done everything right, there will be a cutscene where a shadow stalks the MC.
20. Go up and enter the right side door. Save your game at the upper labs save room.
21. Go up from the upper labs save room and enter a room with a large broken glass and a pool of water. Some dialogue should occur if you are the on the good path. If you want an alternate easter egg cutscene turn back immediately (this will result in the MC going into the room and noticing the nice man tried to hide from her, otherwise you can just move forward and the MC will notice the nice man trying to sneak up on her and invoke stand her ground laws which prompts the nice man to continue to be nice, say some nice things and then leave, there's no difference in outcomes). Go past the broken glass and enter the experimental rooms.
22. A cutscene will occur in which the MC notices a large artery in the room and throws a stone at it which it proceeds to eat. Logically if you attempt to hump the large artery, it will eat the MC and game over you. Go to the right and down to enter a kitchen which has the injured jerk scientist from the captive girl cutscene and talk to him.
BONUS: Go into the upper door in the artery room to find a sewer area with respawning rats. Kill the rats (use the knife if you have it from your second visit of the laptop room) and they occasionally drop keys. You can get basically unlimited keys from these guys. Just keep in mind that until you kill you the next boss, you are unlikely to really be able to cash out on your keys. Since food is a time limit, you may wish to avoid farming excessively for now.
23. Save your game at the upper labs save room and equip the magnum or whatever other good gun you have. Go through the broken glass hole and fight the heart boss. You are expected to shoot the worms its spawns and then follow up by shooting its red eye that opens before it does a poison spray. Do not go under the boss as this will instantly kill you. Use antidotes or vital vials as needed. This boss is easily the hardest in the game aside from optional bosses and the final boss (potentially if you haven't bothered to farm). Once this boss is dead, the artery in the artery room will recede and you can enter goodie bonus rooms which contain a vending machine that trades keys directly for items (including food), a dead dude with SMG and a keycard that lets you access the heart of the laboratory area. Also go back to the kitchen area and hear the dying words of the jerk scientist.
BONUS: Explore the lower laboratory area more closely and you will find an egg room (this is the room above the part where the scientists die and spawn nematodes). Approach the eggs to trigger a fight with the worm boss. Kill the worm boss (much easier with an SMG or magnum). Take the key that is in the room. You can then take this key to the leftside building foyer, then down the stairs and to the doors to the right of where you got your first handgun and fight the slime boss. You can kill the slime boss by climbing the ladder, running towards the red barrels to trigger the grabbing hand and then running left until the hand goes away. Once the hand attack is on Cooldown, go to the red barrels and rapidly tap Z to push them over the ledge. Then shoot the red barrel. Repeat three times until the boss exposes its red core. The boss will shoot the arena and make the upper floor more dangerous by covering it in fire. Keep shooting the red core (use the safe section of the upper floor for healing and safety) until it dies. I have no clue what the benefit of killing this boss is.
BONUS: Exploring the rooms near your starter cell room will lead to a long hallway that has a fast and deadly black slasher in it. He deflects bullets fired at him but can still be headshot when he is preparing to lunge (he is very likely to kill you if you try to exploit this) or if you use the SMG (he only deflects one bullet, the rest go into his face). Shoot him in the face until he dies. Take the key that is the blue hole in the wall. Go back the upper labs goodies room and unlock the door near the vending machine. Take the blaster and trade your keys for energy ammo if you want. You don't need more than 5 or so rounds. Its an instant screen clearing weapon.
24. Go back to the room below the upper labs save room (save your game, equip blaster if you have it and your best guns [SMG or Magnum] with loads of ammo [Pick magnum if you have over 50 magnum rounds otherwise stick with SMG, if you don't have blaster than take both magnum and SMG]) and go through the bottom left path. Open the black doors and head left (previous version of the game would let you explore this area only to be immediately shot dead by sentry turrets, correct me if I'm wrong but this version of the game prevents you from humping the sentry turret room too early and getting shot for it). Go past the computer room and into a big room with a red and green cabinet. Go through the ominous entrance to start the final boss. Assuming you have done everything you should be able to fight the final boss. Just shoot the different appendages of the final boss and try to avoid attacks. The opening phase with the two worm spawners and a second shooty head that spawns electric jellyfish should be fairly easy to beat with just your guns. After that you should bump into a evil human head thingie and just shoot that thing and dodge its relatively easy attack. Then comes the final phase where a giant evil worm mouth thingie comes out. Nuke this with your blaster if you have it. Otherwise drop down to avoid the artillery attacks but quickly head back up to avoid its cheap beam attack. If you have a lot of vital vials, consider tanking the artillery to prevent any chance of being cheap killed by the beam attack.
25. Once the boss is dead, save your game (duh) and head back the air control tower. A cutscene will trigger where the nice man decides he's had enough of the evil lab people and goes rambo on their asses and tells the MC to go blow up the island.
26. Go back to the heart of the laboratory and access the computer that was found on your way to the final boss. Start the self destruct sequence (no timers though, take your time). head back to the air control tower.
27. The MC should be intercepted by evil lab people who force her to drop her cool guns that could have completely obliterated them (and also prevents a new game plus since the MC basically would start with nothing). Go through the stealth sequence (its fairly rudimentary and aside from bad broken gear system controls of the MC its not very hard. Also you get unlimited retries). Go into the air control tower to save (if you wish) then go to through the hidden pathway in the hill above the air control tower and escape on the boat (Megumin wasted her explosion on the evil lab person who tried to GTA the boat). Somehow the MC knows how the drive the boat, I assume she got her boating license from the same online system that jontron used. Boats are just that easy to pilot even when you are underage and have no fucking clue where you are going.