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

Temple Grounds - To Torvus

• Go to Temple Assembly Site and get POWER BOMB TANK 1 via this wallcrawl. Get back in bounds in Dynamo Chamber and go to Great Temple.
• In Transport B Access, after killing the second light enemy with a dark beam shot, use a ghetto jump off of the diagonal bars to get MISSILE TANK 5 from below, where you're supposed to pop out. If you don't want to use the ghetto jump, then get this missile tank the intended way via the morph ball tunnels in the wall.
• Go straight in Temple Sanctuary, unlock the Amber gate, and equip light beam. In Transport C Access, shoot the crystal to move the wall and take the elevator ahead to Temple Grounds.
• Open the amber gate in front of you (it's actually a violet gate, because the game is lying with the color), then follow the path forward.
• In Hall of Eyes, take the dark portal to Base Access. Go to Abandoned Base and use the ghetto jump for Dark Suit Skip to get to the light portal quickly. This is a major run-killer where missing the jump more than a few times will kill you; be sure to practice it before doing runs.
• In Path of Eyes, follow the path forward. Skip the two pirates in front of you (they turn into dark pirates) by just space jumping over the block. Turn, jump over the next block, kill the next pirate on the higher ledge with a dark shot. In this pit here, there are two blocks with dark crystals. Move them both with light beam; you'll be using this path at the very end of the game. Ghetto jump off of the slant in the wall to get to the higher ledge. When facing the pit of water, there is an invisible ledge on the left wall, so jump from there to skip moving the platform in the puddle. Scan the amber gate and make your way to the elevator to Torvus Bog.

Count (17%): 2 E-Tanks, 35 Missiles, 1 Power Bomb, 100 Beam Ammo

Torvus Bog - Beginning

• In Torvus Lagoon, go to the dark door in the water and follow the path to Great Bridge. Use a BSJ to get on the ledge by the light door. Use your power bomb to blow up the denzium on this ledge to get POWER BOMB TANK 2. Either use your second power bomb at the other end of the tunnel to go to the top purple door to Temple Access, or roll back to the light door, stand on the scan terminal, and scan dash off of the eye in the tree.
• In Torvus Temple, have a charged light beam shot ready.
  • Shoot the generator in the ship that flies in to destroy both it and the two pirates riding it instantly.
  • Have a charged dark shot ready and aim up where the flying pirates will spawn; the moment you see the circular reticule, release your dark shot as it will auto-aim on one of the flying pirates. If you shot it early enough, the ooze will freeze the other flying pirate; kill it with a missile. If you failed to kill the flying pirates with this, then use missiles from far away as they home in.
  • You'll face four grounded pirates here. Kill them all with dark beam, then get SUPER MISSILES.
• Make sure you have at least 5 missiles, then take the elevator up and blow open the green door. Go get EMERALD TRANSLATOR and go back down to Torvus Temple.
• Make sure you have at least 10 missiles, as you will blow open two green locks consecutively. Go through the dark door to Temple Access, then blow open the second opening to fall into the tunnel for ENERGY TANK 3. Roll left, blow open the green door, and enter the lower floor of Torvus Temple. Scan the emerald gate as you make your way to the other side, then go to the small elevator leading to Lower Torvus.

Count (21%): 3 E-Tanks, 35 Missiles, 2 Power Bomb, 100 Beam Ammo

Lower Torvus Bog

• In Hydrodynamo Station, use [[Metroid_Prime_2:_Echoes/Early_Items#Gravity_Boost|underwater dashes] to go down to the bottom part of lower Torvus and get GRAVITY BOOST early.
• In Main Hydrochamber, after getting gravity boost, skip the Alpha Blogg fight.
• In Hydrodynamo Shaft, kill the little fish with a charged light shot to refill on health, missiles, dark ammo, and power bombs, then float up to the dark portal to go to Undertemple Access.
• Climb up the stairs and use a power bomb to blow open the yellow door at the top of Undertemple Access.
• In Undertemple Shaft, climb up to the top with the morph ball cannon in the upper center. Heal at the save station if you must. Fall to the grated floor and go into the opening with a light crystal. Either bomb the slot in the center to rotate the structure, or scan dash to go to the blue door that leads to Sacrificial Chamber Tunnel.
• In Sacrificial Chamber Tunnel, roll until you pass the first four caches, then blow them up; the next room with Grapple Guardian is loading. Suck in all the drops, destroy the remaining caches if needed (you want to have at least one power bomb), then go into Sacrificial Chamber.
• Defeat Grapple Guardian and get GRAPPLE BEAM. Be sure that you blew open the gate to the light door during the boss's transition first; if you have an extra power bomb, blow open the gate to the dark door. Go through the light door and get MISSILE TANK 6 in Undertransit One, then return to Sacrificial Chamber. Go through the dark door and two rooms ahead, take the light portal back to the light world.
  • If you don't have any power bombs after the fight, and still need to blow open the gates, you can reach the grapple point from the bottom floor via just space jumping. Go to Sacrificial Chamber Tunnel to get power bomb refills from the caches.
• In Catacombs, fall out of this alcove by moving back and left, then activate the underwater bomb slot below. Make sure you have a power bomb, and blow open the caches straight ahead to get some. Take the dark door and follow the path back to Hydrodynamo Station, then take the elevator back up to Upper Torvus.

Count (24%): 3 E-Tanks, 40 Missiles, 2 Power Bomb, 100 Beam Ammo

Upper Torvus Bog

• In the lower floor of Torvus Temple, head left through the door that was behind the emerald gate you previously scanned. There is a missile tank below the grate in the next room; ignore it, as you'll get it with boost ball during cleanup.
• Go through the light door to Torvus Grove, take out the dark grapple pirates if they spawn, then approach the door on the other end. The lasers will block you and two pirates commanders will appear. Plant a power bomb below the center of the tree to take out the pirates and the tree trunks to uncover a missile tank (you'll get this during cleanup with screw attack and boost ball). Be careful not to get hit by the phazon crates.
• Take the scan portal in Meditation Vista to the dark world.
• In Polluted Mire, climb around the platforms. You can skip the platforming parts here by either:
  • Doing a BSJ on the third platform to reach the dark door
  • Stand on the fourth platform and scan dash off of the bottom door to reach the dark door
• Heal at the save station. Jump on the save station and go to the upper door to Dark Forgotten Bridge.
• Follow the path to Dark Torvus Arena. Clear the three dark preeds in this room with light beam first, then kill Boost Guardian with a power bomb to get BOOST BALL. Get the second Dark Torvus Key with boost ball and go back to Dark Forgotten Bridge.
• Just when you enter, go to the alcove on the left and do a 3BSJ to get out of this hall. Light beam the beacon in the center of the bridge, as a grapple pirate appears there if they activate. Blow open the green door with a super missile and scan dash to it; take out grapple pirates from this ledge if they spawn.
• Follow the path to Venomous Pond. Use either a scan dash or the grapple point to get the third Dark Torvus Key. Go into the Dark Torvus Temple.
• Before going into the hologram, go behind it to get ENERGY TANK 4. Use the ammo station nearby, as Chykka is very ammo intensive.
• Defeat Chykka to get DARK VISOR.
• Climb up the platforms in Dark Torvus Temple, and go to Dark Controller Access. Bomb the slot, then bomb it again to reload the room with Chykka; do NOT get the torvus energy! You can now just leave Dark Torvus Temple.
• In Venomous Pond, go forward through the dark door. In Portal Chamber, roll through the tunnel, and on the other side, climb over to go to the light portal here, healing if necessary.
• Grab MISSILE TANK 7 directly in front of you. Ghetto jump off the floor to get out of bounds here and do a quick wallcrawl to Torvus Lagoon then Path of Roots. Either ceiling warp in Path of Roots, then BSJ up to MISSILE TANK 8, or be quick and let the room load around you at the missile tank (this is very risky though and can get you stuck, softlocking the game).
• In-bounds, get to Torvus Lagoon then take the elevator back to Temple Grounds.

Count (29%): 4 E-Tanks, 50 Missiles, 2 Power Bomb, 100 Beam Ammo

Temple Grounds - To Sanctuary

Lower Sanctuary Fortress

Upper Sanctuary Fortress

Temple Grounds - To Light Suit

Lower Torvus Cleanup

Sanctuary Cleanup

Agon Cleanup

Upper Torvus Cleanup

Temple Grounds Cleanup