4% Current Route

Before moving forward, I feel that it's necessary to lay down some groundwork about the run.

Disregarding the rest of the game, beating the final bosses requires requires only four items:
Light Suit, for surviving EI3.
Screw Attack, for entering and leaving the EI Arena.
Morph Ball Bombs, for damaging EI2 among other things.
and Spider Ball, for climbing EI2.

By skipping the Item Loss sequence and triggering it later in the run, you can reset the percentage counter and your inventory. Miraculously, as long as you've done everything you need to before Item Loss, it's possible to finish the rest of the game with only those four items. It used to be thought that you would need items like Space Jump, Dark and Light Beam, and Boost Ball, but through a lot of glitching it's possible to skip every item that isn't absolutely required in the Sky Temple. 4% really shouldn't be possible, but it is.

Aside from blowing up Blast Shields and Translator Gates and the like, there are three main objectives that must be completed during Prelude:
1: All 9 Sky Temple Keys must be popped but not collected. There are two in Agon, two in Torvus, two in Sanctuary, and three in Temple Grounds. Popping Key Pods requires killing the Chykka to get the Virtual Boy.
2: Screw Attack must be unlocked but not collected. This requires killing Caretaker Drone to activate a load trigger in Main Research, opening the portal in Watch Station, and solving the puzzle in Vault.
3: Light Suit must be unlocked but not collected. This requires killing Quadraxis to get the Annihilator and returning Sanctuary's energy.

It's pretty fun to play around with the routing and I encourage everyone to try to come up with a cool custom route, but any route must do those three things during Prelude (along with opening the gates required for your custom route).

Do Item Loss Skip and wallcrawl to Seekers. After wallcrawling to Seekers, do ILS again and go do Early Power Bombs. Along the way, scan the elevator in Hive Transport Area and blow open the gate in in Industrial Site. Get the E tank and the Missile before heading to Agon.

Once in Agon, head to pirate fortress and collect dark beam and then collect light beam. If you're going inbounds, DON'T LOWER THE GODDAMN SAND. Make sure to collect the Energy Tank in Mining Station Access, and if you want you can also collect the Energy Tank in Bioenergy. When you travel through Dark Oasis, blow up the wall.

After getting Light Beam, collect the two Pirate Fortress Agon Keys and then head to Amber Translator. After getting Amber you want to head to Portal Chamber to collect Dark Suit, but you could also go collect the Energy Tank in Mine Shaft.

After getting Dark Suit, hit both of the bomb slots in dark portal chamber and in transport center and head to Torvus.

Once in Torvus you need to collect Super Missiles. You can just go inbounds which is the easier strat, but it's faster to wallcrawl straight from the elevator to Torvus Temple.

After collecting Supers, collect Emerald. It's faster to take the elevator in Torvus Temple, but if you want the tank in Temple Access now is the time to get it (if you're going for segmented, you should scan the elevator even if you're getting the E tank). Either way, make sure to blow open the Super Gate that leads to Temple Access and lower the translator gate before heading to Lower Torv. In Lower Torvus, to the puzzle in Hydrodynamo Station and get Gravity. Go through the portal in Hydrodynamo Shaft, get the key, and fight Power Bomb Guardian. Then leave to the portal in Undertemple Shaft.

Leave Lower Torv. Head to Torvus Grove and then the teleporter in Forgotten Bridge.

Collect the key in Arena and then head to go fight Chykka. Pick up the last key along the way. If you want to, pick up the E tank in Dark Torvus Temple.

After killing Chykka, go to Putrid Alcove to get oob and use the Virtual Boy to pop the keypod in Poisoned Bog. Then go back inbounds and leave the Dark World through Portal Chamber. Do the secret world and then ceiling warp into Torvus Lagoon.

Make sure you have at least 2 power bombs before leaving Torvus. Older routes had problems with Power Bomb management here, but you should with the current route. It's still worth mentioning. Head to Temple Grounds and then go through Windchamber. Pick up the E tank too (DON'T EVER SKIP THIS E TANK. THIS IS THE MOST IMPORTANT E TANK IN THE ENTIRE RUN). Once you reach GFMC Compound, go to the portal in Sacred Path. Make sure to collect a power bomb in Sacred Bridge along the way. Pop Reliquary.
https://www.youtube.com/watch?v=4M0Dznx6djs

NOTE: that strat is kind of obnoxious and RNG dependent and unfun bullshit. That can be mitigated with more E tanks. 2 is heavily RNG dependent, 3 is slightly RNG dependent but generally pretty consistent, 4 is generally pretty consistent with no RNG dependence (farming for drops isn't necessary and you can boost out the way you came), and 5+ is really consistent if you practice a couple of times and know where the spots are. If you really don't want to do this there is a time to come later with Cannonball so this isn't necessary.

Get Violet, scan the gate leading back to Sacred Path and the gate leading to Temple Assembly Site, and then head to the elevator that leads to Agon.

If you're going for segmented completion or doing the Cannonball strat for Reliquary, you also want to do the gate leading to Meeting Grounds and activate the Light Block.

Shoot the Light Block in Temple Assembly Site, then pop Lake.

IMPORTANT! If you have scanned the thing in Industrial Site that moves the giant thingy, then you MUST lower the bridge before item loss.

Once in Agon, head to Portal Chamber and go to the Dark World (it's probably faster to use the Portal in Transport Center, but Transport Center is annoying). In the Dark World, pop the keypod in Battleground and then go to Feeding Pit. Do Feeding Pit SW, wallcrawl to Oasis and pop the key there. BLOW UP THE WALL IF YOU HAVEN'T ALREADY. This is your last chance to blow it up. Make sure you have at least 1 power bomb, ideally 2 before going to the light world and heading to Sanctuary.

In Sanctuary, DO NOT SOLVE MINIGYRO PUZZLE. DON'T. DON'T. DON'T. Use a power bomb on the tube and enter the portal.

Go up to Hive Dynamo and open the portal. Go out of bounds and pop Hive Dynamo. Wallcrawl down to Hive Entrance and pop the pod there. DO NOT HIT TERMINAL FALL. Clip back inbounds and head back up. Along the way, BLOW UP THE BLAST SHIELD IN HIVE REACTOR.

Go to the light world, then immediately get oob in Dynamoworks then wallcrawl up to the PB door in Main Gyro Chamber and get the wifi adapter. After getting the wifi adapter, head to Watch Station Access and pick up the E tank. Then go to Sentinel's Path and get oob to wallcrawl past Grand Abyss. DO NOT TRIGGER THE ROBOTS. DO NOT. YOU NEED THEM IN LIKE 3 MINUTES

In Vault, DO NOT LOWER THE BRIDGE. LOWER BRIDGE = RUN DED.

Dash to the platform then solve the puzzle. DO NOT PICK UP SCREW ATTACK.

Enter Grand Abyss, and do Reverse Grand Abyss.

Do the puzzle in Watch Station, then go to the portal in Dynamo Works. You can either get oob in Hive Dynamo and wallcrawl to Quad, or you can go inbounds and do a BSJ. Either way kill Quad and get Annihilator.

This is the hardest part of Prelude. You have to dash to this tiny pole sticking out of the wall. It's really precise and annoying and is why you want so many E tanks.

After getting this dash, head to the light world through Watch Station and use the portal in Dynamo Works, and do Post Quad Quad Skip. Steal the planet's energy and then do the dash again.

After doing the dash again, head to the Light World. Return the planet's energy and get Cobalt. Then scan the Cobalt gate in Sanctuary Temple and leave to Watch Station. DO NOT ENTER A CANNON IF YOU GOT CANNONBALL. It is ok to enter the Central Flow Chamber in Hydrodynamo, but nothing else.

Enter the portal in Watch Station and dash over to the door to Central Hive Transport West (If you don't want to do the dash in Aerial Training Site, you can go through Central Area Transport West, but that's slower and I seem to recall hearing that it can crash the game). Solve the wifi adapter puzzle in Staging Area and then fight Caretaker. After killing Caretaker, kill the bot in Central Area Transport West and then head to Torvus.

Once in Torvus, go to the portal in Hydrodynamo Shaft. Go up to Undertemple Shaft and then go OOB and pop Dungeon. Leave through the portal in Dungeon then go to Upper Torvus and then leave to Temple Grounds

Head back to Great Temple and then head to Meeting Grounds. Break off the blast shield in Hall of Eyes and then make sure that the door opens (the shield exists on both sides and you need it gone on the other side. It only disappears on the other side if the door opens). Use the portal in Hall of Eyes. Go pop defiled shrine, and along the way break every Blast Shield. At this point you should be ready for item loss. You should have popped all 9 keys at this point, unlocked Screw Attack, and unlocked Light Suit.

HAVE ANNIHILATOR EQUIPPED. PRESS C-DOWN BEFORE ENTERING THE PORTAL AND TALKING TO DARK SAMUS.

Talk to Dark Samus and convince her to take away all of your shit. This includes Cannonball.

She does a shitty job taking away all of your shit and she doesn't dequip Annihilator. DO NOT EVER PRESS UP ON THE C STICK BEFORE KILLING EI3. C-UP = RUN DED.
If you did not lower the bridge in Industrial Site, then you have to ghetto jump onto the giant thingy and then ride it during the cutscene up to the ledge. If you're a dummy like me and skip the cutscene too early or forget to lower the bridge, then run = ded.

Go to Great Temple and get Light Suit (1%). Unfortunately, all of the Temple Energy Controllers require bombs to leave, so you can't really use the light rails yet. Head down to Temple Assembly Site and then Agon to go get bombs.

Just kidding. Bomberman is immune to Annihilator type damage, so you can't get bombs yet. Do Sandigger and then wallcrawl to Sanctuary to go get Screw Attack. Do once in Sanctuary, dash up to the ledge in Hall of Combat Mastery, and then do Minigyro SW and wallcrawl to Main Research. Transition to CATW, and then aether jump up until it proximity loads Watch Station. Quickly morph and then walk over to the door to door warp Main Research, then head up to Watch Station.

Enter the Dark World in Watch Station, and then do Judgement Drop and wallcrawl to the Portal.

In Grand Abyss, use the terminal fall to climb up the platforms and then go collect Screw Attack. Screw Attack across Grand Abyss and then head to Sanctuary Temple. Go OOB and collect Cannonball. Then wallcrawl to Sanc Energy Controller and use the light rail to go back to Great Temple. NOW head down to Temple Assembly Site and then Agon to get bombs.

Use Screw Attack to kill Bomberman. After getting bombs, you're finally ready to start collecting keys. Go to Portal Chamber to get out of Bounds. DO NOT ENTER THE CANNONS. DO NOT.

Do Portal Chamber SW and go collect Battleground. Do Portal Chamber again and collect Oasis. Escape Oasis and then leave to Temple Grounds.

Use the portal in Temple Assembly Site and then go collect Lake. Go up to Great Temple then head down to Sacred Path. Go collect Reliquary. Head back to Great Temple and then go to Sanctuary. Go fight Spider. DO NOT USE THE CANNONS. DO NOT.

Kill Spider, then go out of bounds and enter the Dark World. Collect Hive Dynamo Works, then go out of bounds and wallcrawl to Central Hive East Transport. Ceiling warp into the right side of the room and then get stuck inside the collision. Build up angular momentum for 55 seconds and then use that to touch the load trigger. Enter FPS.

FPS deserves a pastebin of its own, but here are the important things to keep in mind.

DO NOT MORPH. MORPH = NO MINIMAP. MORPH = MAP CRASHES GAME. DO NOT MORPH.

DO NOT HIT TERMINAL FALL AT ANY POINT. TERMINAL FALL = RUN DED. Unseen Way, Hive Reactor Access, and Hive Entrance all have terminal fall.

Use the blue triangle that appears when you press L to determine your camera angle and whether or not you got an Aether Jump.

Transition to Culling Chamber. Aether Jump onto the ceiling of the room, then fall down to the door. If you enter the skywalk, walk over to Unseen Way's box to fall back down. DO NOT MORPH.

Use Screw Attack to transition to Unseen Way.

Go to Unseen Way's skywalk, then proximity load Reactor Core and land on the door. Transition to Reactor Core, and then jump down and proximity load the save station to unload Unseen Way, then walk back into the Aether. If all goes well, you won't fall very far down into the Aether. If you're well above Hive Reactor Access, just walk around the room and go to the door. If not, get to the bottom of Reactor Core's box, proximity load Hive Reactor Access, then Aether Jump to the top of Hive Reactor Access' box.

Wiggle along the wall to proximity load Entrance Defense Hall, then Aether Jump to Entrance Defense Hall.

Jump to Entrance Defense Hall's ceiling, then slide along the ceiling until you hear yourself hit a standable spot near a corner. Jump to the other corner, then jump over to the door. Transition to Entrance Defense Hall, then Aether Jump up to the skywalk. Float until you're above the platform where the key is, then proximity load Hive Entrance and have the platform load underneath you. Collect Hive Entrance, then jump down. Aether Jump back up and load Hive Reactor Access. Transition to Hive Reactor Access, then go up to the skywalk. Float for about 30 seconds, and then warp into Hive Reactor.

DO NOT TOUCH ANY OF THE PURPLE SHIT. TOUCHING PURPLE SHIT = GAME CRASH.

Go to the door and morph and roll through it. Hopefully, you won't crash the game and won't lose minimap. Find the Save Station to restore your eyesight.

Leave to Hall of Combat Mastery, then wallcrawl to Transit Station and warp. Leave to Torvus.

Go to the portal in Main Hydrochamber, then climb Undertemple Shaft. Go out of bounds in the save station, and wallcrawl to Dungeon. Collect Dungeon. Go back to Catacombs, then do Transit Tunnel South SW and wallcrawl out. Head to upper Torvus and enter the portal in Portal Chamber. Collect Poisoned Bog and go back to the portal from when you came. Do Portal Chamber SW and then get back inbounds and head to Temple Grounds. Enter the portal in Hall of Eyes.

Collect Landing Site, then enter the Sky Temple.

Kill Emperor Ing.

Press C-Up. Leave Sky Temple and then kill Dark Samus.