The definition of 100% is item collection of all 100 distinct items. This means that ILS cannot be used for this category, as a missile tank does not exist until Samus enters the room where she loses her upgrades at the beginning. The 101% trick is used as it speeds up the early game; the missile launcher is not collected twice for the purpose of increasing the percentage. This is a longer, and more "traditional" category, with less wallcrawling and more in-bound tricks than any%.

Though the routes will not go over room-by-room specifics, notable tricks or sequence breaks will be noted.

Route

Temple Grounds - Beginning

• Make your way through underground Temple Grounds and lose your upgrades. Take the elevator up and make your way to Industrial Site, then Temple Assembly Site.
• Go through Dynamo Chamber, Communication Area, Troop Security Station, then GFMC Compound.
• In GFMC Compound, do the 101% Ghetto Jump to get the MISSILE LAUNCHER twice. Use a ghetto jump by where you blew up the yellow crate to climb up quickly to Sacred Bridge.
• In Sacred Path, ghetto jump off of the square blocks at the left side to get on the hive. Scan dash from the hive on the other side of the room to the left, then get on the wall to the right and scan dash left again to quickly make your way to Great Temple.
• In Great Temple, fight the dark splinters with missiles. Try to hit multiple at a time with splash damage from missiles. You want to be at 0 missiles before killing the last splinter, so the game will usually give you a double missile drop before fighting the Alpha Splinter. Make sure you're at 1 missile after finishing off the Dark Alpha Splinter.
• Go straight and get VIOLET TRANSLATOR. Take the elevator back down, take right at the junction, and go back to Temple Grounds.
• Use your 1 missile to blow open the red door in Temple Assembly Site to get ENERGY TANK 1. Make your way to Transport to Agon Wastes, getting MISSILE TANK 1 behind the web in this room.

Count (5%): 1 E-Tank, 15 Missiles

Agon Wastes - Beginning

• Go to Mining Plaza and climb it. After blowing down the first bridge and just after crossing it, turn right and you can stand on a slanted floor at the very edge. Ghetto off of this to reach the top quickly. Make your way to Mining Station A.
• Carefully climb this room. Kill the space pirates if you want to; they can make you fall off platforms if you're not careful. Go to the red door and make your way to Agon Temple.
• Defeat Bomb Guardian and go get Bombs and Amber Translator. Go back to Mining Station A, and while making your way to Portal Access A, scan the amber gate in Mining Station A.
• In Portal Terminal, kill both pirates and then the dark pirates (use missiles). Solve the puzzle to unlock the portal and go to Portal Site in Dark Agon.
  • The portal puzzle can be completed quickly. The first block can be skipped by carefully rolling against the block and off the edge, then unmorphing to land on the large platform after the first block. The second block can be skipped by jumping from the first large platform and hugging the wall to land on an invisible ledge.
• Go fight Jump Guardian by taking the backwards path and get Space Jump. Head back the way you came back to the light world, making sure your missile count is high to take on the pirate base.
• In Portal Terminal, go to Portal Access A. Roll behind the corpse to get MISSILE TANK 2 before going into the cannon.
• In Mining Station A, go to the door just above you when you enter to enter Sand Cache and get MISSILE TANK 3. Back in Mining Station A, use space jump to go to Central Station Access, then Central Mining Station to enter the Pirate Base.

Count (10%): 1 E-Tank, 25 Missiles

Agon Wastes - Pirate Base

Note: Missile management is important here, as you will be using missiles a lot to kill space pirates quickly, blow open glass and red doors, and fight Dark Samus. Grab every drop you can with charge beam, even if it's health.

• Use two missiles, or charge beam + 1 missile for each space pirate to take them out. When the turrets go up, use a charge beam + 2 missiles for each. When the fight is done, get BEAM AMMO EXPANSION 1 early by a BSJ up the right turret platform, then either rolljumping or scan dashing across the room to reach the higher platforms.
• Bomb the grated floor in the back-left corner in Command Center Access and roll through. In the morph ball tunnels under Command Center, take the right junction to get MISSILE TANK 4, then roll out. Take out the two pirates on the bottom floor, then spawn the third pirate on the top floor and kill it. There are three ways to spawn the third pirate quickly, then go through to Security Station B.
  • The easiest way is to go to the gate blocking the door to Biostorage Access, and jump on the middle. Then jump up to the higher ground. This is reasonably fast if done with a dash off of the second pirate while killing him.
  • By the exit of the morph ball tunnel, do a 3BSJ to climb up quickly.
  • To the left of the portal are a lot of computer monitors. Jump on it, then jump up to spawn the third pirate. Kill it from below, wait a bit, then jump high just when the door-unlocked cutscene plays; if you're high enough, the game will warp you up to the top.
• After watching Dark Samus taunt you, blow open the red blast shield, briefly enter the glass alcove, then roll out immediately. This makes the monitor in the alcove scannable from the outside in Command Center, rather than only inside the alcove. Scan it, then go to Biostorage Station.
• Jump off of the crates to the right to skip taking the elevator here.
• In Bioenergy Production, take out the flying pirates with a charge shot + 2 missiles each (3 missiles if a flying pirate is too far to reliably hit with charge beam). Then climb out of this room.
  • If you want, you can grab the energy tank here first. Do the controller trick to grab it, then manually do the block puzzle to get out of this room. It costs a lot of time, but it also makes the first half of the route much easier for newer players.
• Use the save station to heal up; the next room is loading anyways.
• Defeat Dark Samus 1 and get DARK BEAM.
  • By the time you beat Dark Samus, if you're really low on missiles, then burn them until you're at zero, then blow open the crate by dark beam; you should usually get a double missile drop (if not, blow open the other crates in the room). You want missiles to blow open a few red locks in Dark Agon.
• Go through the dark door and go to Command Center and take the dark portal there.
• In Doomed Entry in Dark Agon, ghetto jump off of the corpse to the left to get on the higher platform (lower it as normal if you have trouble doing this). Take the dark door on the right.
• Follow the path to Dark Oasis and open the blue door on the right; you should bomb the phazon crate, so you get it out of the way for the rest of the run, but be careful not to be in its blast radius.
• In Hall of Stairs, skip the dark beam puzzle by jumping off of the tallest ingpod and going through the door with the red lock.
• Heal in Save Station 3. Before entering the save station, walk past it to trigger the next room to load then heal. If you don't do this, you will be waiting for the next door to load after healing.
• In Phazon Site, scan the terminal on the far left behind the large crates (using either a rolljump to scan it from above, or blow up the crates with missiles). Then scan the terminal on the other side of the room on the higher ledge. Climb on the three moving platforms and scan the last terminal high up.
• In Watering Hole, use either a rolljump or a scan dash off the crystal to skip the platforming part.
• In Feeding Pit, go to the other side of the room from where you enter and shoot the crystal with the dark beam (it's the one closest to the dark door). Ghetto jump off of a slant in the wall to reach the lowered platform and go get LIGHT BEAM. You can skip lowering the platform with the same ghetto jump, but it's much more difficult.
• Take the light door in Feeding Pit and make your way back to Dark Oasis, taking care to manage your health. Take the portal here back to Main Reactor in Light Agon.
• Take the dark door and take the bottom floor path to Central Mining Station. Go to Mining Station A, then Mining Station Access; use bombs here to get ENERGY TANK 2. Make your way back to the elevator to Temple Grounds.

Count (15%): 2 E-Tanks, 30 Missiles, 100 Beam Ammo