The 100% category for Metroid Fusion is the opposite of 1%. Instead of worrying about health and missile management, the player must remember item placements and room strategies, and most of all, 100% cleanup, which is the most difficult segment of the entire category. Samus will end with 20 e-tanks, 250 missiles, and 74 power bombs.

Many new players have the misconception that 100% is easier than any% because the player is forced to have more energy and missile tanks for bosses. However, strategies for both categories are exactly the same; if the player is relying on an overload of expansions to pull them through the bosses, then it is clear that the player does not know how to fight bosses.

It is highly recommended that the player start with learning Any% first, as most strategies and skills learned in Any% will easily carry over to 100%.

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Leaderboards for Metroid Fusion 100% can be found here

Full Route

Each section of the game will have a counter of how many energy tanks, missile tanks, and power bomb tanks the player should have by the end of it. It is also recommended to be playing on a New Game+ file, as the game provides a checklist of how many of each type of expansion Samus got in each sector, or in the entire game.

It is assumed that the player is familiar with the any% route, and is familiar with the locations of the expansions.

Abbreviations: ET = Energy Tank, MT = Missile Tank, PB = Power Bomb Tank

Main Deck Beginning

The route is the same as Any%, past obtaining the main Missile upgrade. Collect MT1 and MT2 the same way as in Any%, in the dark vertical shaft.

Collect both ET1 and ET2 before Arachnus. ET2 can be found by missiling the leftmost block of the right part of the ceiling before falling into the fight.

Because you have used one missile for ET2, Arachnus is more difficult than in Any%. It is important to make sure you have enough missiles for the core-x.

Collect MT3 after the navigation room with morph ball, just as in Any%.

Count: 299 Health, 25 Missiles

Sector 1 - Charge Beam

There are many obtainable missile tanks in Sector 1; however, it is faster to collect all of them during cleanup.

The route here is the same as Any% except to also collect ET3 in the toad room after the first stabilizer.

Count: 399 Health, 25 Missiles

Sector 2 - Bombs & Hi Jump

The route up until collection of Bombs is the same as Any%.

After leaving the Bomb Data Room, get MT4 in the top right corner by bombing the blocks.

In the next room, do a walljump to reach the hidden morph ball tunnel in the top-left corner. Bomb the floor to reveal a pillar to reach MT5.

Two rooms ahead, fall into the bottom-left pit with the blue zoro. Collect MT6 here by bombing the bottom-right corner of the pit. Be careful not to take more than one hit from the blue zoro, as it does enough damage to kill you.

Follow the Any% route, but get ET4 in the room just before Zazabi.

After Hi-Jump, you can skip the SA-X encounter by intentionally being frozen and hit by a super missile (this does a total of 300 damage), abusing the mercy invincibility to run through SA-X and either escape safely or spin jump over the ice beam shot it fires at you. If you are frozen a second time, you have a very small time window to jump before the super missile hits you, assuming you ran far left; however, you'll be left with 1 HP. This skip not recommended for newer runners though, and is somewhat luck-dependent.

Leaving Sector 2 after Hi-Jump follows the same strategy as Any% besides the SA-X skip.

Count: 499 Health, 40 Missiles

Sector 4 - Speed Booster

Follow the Any% route until the path splits with two doors on the left side. Instead of taking the bottom door, take the top door and follow the long path to collect ET5.

Return to the fork, take the bottom door, and after crossing the water, go to the room above and climb into the hidden morph ball tunnel on the left to collect MT7.

Follow the Any% route until after obtaining Speed Booster. After breaking the speed boost blocks immediately after Serris, instead of falling all the way down, reveal the morph ball tunnel on the left wall to find both MT8 and MT9.

After lowering the water level, get MT10 immediately below the switch. After speedboosting through the hidden path on the bottom of sector 4, shinespark through the pond above with MT11 in plain sight.

Leave Sector 4 as normal.

Count: 599 Health, 65 Missiles

Sector 3 - Super Missiles

In the room before unlocking Level 2 Locks, get MT12 below the breakable floor in the middle of the hall.

MT13 is BOB, the unskippable missile tank. You can't miss it.

After obtaining super missiles, run through the left hall and fall into the pit with the save room and recharge room. Get MT14 in the far right using super missiles.

Fight BOX and leave Sector 3 as normal.

Count: 599 Health, 80 Missiles

Sector 6 - Varia Suit

After running through the first hall with the flies, remember to plant a bomb on the bottom left corner of the room with the super missile barrier.

Follow the Any% route up until escaping SA-X, including collection of ET6 before the encounter. The room after escaping SA-X, roll into the bottom-left corner of the room to enter a room with several worms and MT15 in the top left corner.

Fight Mega-X as normal. After climbing the vertical shaft after Varia Suit, go left instead of right, get the MT16 over the crumble blocks, and MT17 in the left tunnel while falling through the crumble blocks.

On the way back to the navigation room, in the room that had the super missile barrier, remember to bomb the bottom right corner, and also get MT18 in the bottom left corner where you should have bombed earlier at the start of Sector 6.

Count: 699 Health, 100 Missiles

Sector 5 - Ice Missiles

Follow the any% route until collection of ice missiles. In the vertical shaft after the ice missile data room, go to the bottom-right corner and get MT19 with the ice missile puzzle. The rest of the route is identical to any%.

Count: 699 Health, 105 Missiles

Meltdown

Identical to Any%. You don't collect any expansions during or returning from meltdown.

Count: 699 Health, 105 Missiles

Save the Animals

Identical to Any%. Collect MT20 and MT21 like in any%.

Count: 699 Health, 115 Missiles

Sector 5 - Power Bombs

After getting Power Bombs, get ET7 below the data room with either a precise walljump or by freezing the ripper near it.

After the SA-X escape, plant a power bomb as high as possible to both be able to collect PB1 and unlocked the vertical shaft above to PB2.

After the hall with shooting the gate by the save room, power bomb the barrier above to enter a puzzle room with crumble blocks, two rippers, and PB3. Head to the main deck as usual.

Count 799 Health, 115 Missiles, 16 Power Bombs

Main Deck - Space Jump

After the room with frozen Ridley, inside the dark spitter room, plant a power bomb to unlock tunnels to the left for PB4. Head right, and whether you get the speed boost or not, plant a power bomb to uncover MT22. Head back to the ship like normal.

Get ET8 in plain sight on the path to Yakuza, as well as MT23 in the morph ball tunnel in the room before Yakuza. Fight Yakuza like normal, and escape from the SA-X like in any%.

Count 899 Health, 125 Missiles, 18 Power Bombs

Sector 2 - Plasma Beam

In the giant empty room two rooms after escaping SA-X, get PB5 by the red glider enemies, before the save room. Continue to Nettori.

Nettori is one of two bosses where the 100% strategy differs significantly from Any%. Because you have so many missiles, it is best to simply use missiles for the entire fight, as firing only missiles is the best human form of DPS at this point in the game.

Laying power bombs in between missiles is theoretically faster, but for a power bomb to save time, it must be planted before the cooldown of the previous missile is complete. In other words, it will waste time for real speedruns (But used in TAS).

After climbing up the vertical shaft after Nettori, go right instead of left to get ET9.

When returning to the main room of Sector 2, there are two route choices the player can make, which is discussed in further detail here (insert link).

If you are taking Route #1, then drop down and around to the left door that leads to the vine room missile tank to get MT24. Go to the navigation room immediately after.

If you are taking Route #2, then go to the navigation room like normal in any%.

Count 999 Health, 130/125 Missiles, 20 Power Bombs

Sector 5 - Gravity Suit

Do the nightmare shinespark like in any%. When entering the water for the first time, hug the left wall and plant a missile at the correct spot to reach ET10. The missile block leading to the ice room is on the same height as the grabbable spot on the right side, so use that as a visual cue.

After exiting the water, go through the ceiling enemies and head to the left room. Plant a power bomb to uncover PB6. Exit the room, and put a power bomb high up to uncover a path at the top of the room to PB7. Head for Nightmare as in any% and get ET11 in plain sight just before the fight itself.

After obtaining gravity suit, and reaching the deep underwater sector 5 area, before entering Sector 4, speed boost through one layer of blocks on the right, and shinespark up for PB8. Head for Sector 4.

Count 1199 Health, 130/125 Missiles, 26 Power Bombs

Sector 4 - Diffusion Missiles

Immediately below the first save room is a hall with several shelled enemies and MT25; get this upon entering lower Sector 4. Go to the opposite side of the door of this hall and climb through a hidden morph ball tunnel to get PB9.

When breaking the first left glass tube like in any%, after climbing up through it, get PB10 through the top right corner. Go unlock Level 4 doors as normal.

After unlocked Level 4 Locks, in the middle of the vertical shaft is a hidden tunnel to the right. Go through it, use a power bomb to kill the crabs in the bottom left corner, then charge beam to kill the two golden crabs that spawn after. Get ET12 in the door that opens. Exit this area.

When running through the second glass tube like in Any%, use a power bomb to break it to get MT26.

While using the shinespark shortcut like in any% to shinespark through the vines in lower sector 4, get MT27 and PB11 in sight behind speed boost blocks.

After getting Diffusion Missiles, go to the bottom left room of the room with the spike-ball bugs and get MT28 behind the super missile barrier. After that, in the big room by the recharge room above, head left two rooms and use power bombs to get PB12 in the very bottom of the giant water room. You should have every expansion sector 4 by now. Go to the navigation room.

Count 1299 Energy, 150/145 Missiles, 34 Power Bombs

Sector 6 - Wave Beam

In the first giant room of Sector 6, after the hall with the bugs, go to the bottom-right orner with the wall that you bombed after obtaining Varia Suit and get ET13. The rest of this segment is identical to any%.

Count 1399 Energy, 150/145 Missiles, 34 Power Bombs

Sector 1 Cleanup

After escaping from the Restricted Sector, talking to Adam, and going up the following elevator, use a charged diffusion missile into the center wall by the rippers to uncover ET14.

In the room after the acid room, shoot down to uncover a hidden room below. Use a charged wave beam shot to kill the crab enemy, then a diffusion missile on the ceiling jet enemy that spawns, then kill the golden pirate that spawns from that. Head right to get PB13. Leave this area and fight Ridley like in any%.

When returning to Sector 1, after space jumping up the first long vertical shaft with space pirates but no platforms, head to the right door instead of the left door (any% goes left). In the room with the third stabilizer you destroyed at the start, go to the top left door for MT29.

Climb the vertical shaft on the right, and on the third room to the left (this is the room that had the eyedoor before Charge Beam), screw attack the bottom-right blocks and the bottom blocks of the center wall. Run left, shine charge and shinespark right, then shinecharge before falling into a water room. Quickly screw attack down (killing the crab), and shinespark up along the right wall to get PB14.

Charge a shine the same way you did before, except this time, head into the room where you got charge beam, shinespark into the slope, then shinespark along the left wall to find ET15. Take the top-right door, and fire a charged diffusion missile into the top left wall to uncover a path to a room with several crabs and MT30.

Go through the stabilizer room following the charge beam room, go through the gate, and go to the save room. Shoot the crack in the wall to find a vertical shaft with MT31. Leave the save room, take the top left door, then the lower left door, then keep running to speed boost through the door. At the top of the next room (the top of a vertical shaft with space pirates), shoot the door and shinespark left to reach the lava room with MT32, MT33, MT34. You'll shinespark through one missile tank, finish shinesparking by the second one, and then get the third missile tank in the bottom-right corner in the lava. Take the green door.

If you took Route #1, climb out and go to the top right door to reach the first big room of Sector 1. Take the blue door at the top-right corner, screw attack the ceiling to get PB15. Return to the left lava room and take the shortcut to Sector 3.

If you took Route #2, you will leave PB15 for the end of Sector 2. Instead, immediately go to the top left to take the shortcut to Sector 3.

Sector 1 should be cleaned up now, except for the aforementioned power bomb tank if you took Route #2.

Count: 1599 Energy, 180/175 Missiles, 40/38 Power Bombs

Sector 3 Cleanup

Don't stop running through the shortcut. When you enter Sector 3, Space boost left to go through the screw attack blocks and the speed boost blocks by MT35. Drop down, and start running left, killing all the enemies with either spammed diffusion missiles or well-timed charged wave shots. In the next room, space boost or shinespark through the wall. Plant a power bomb, and while waiting for it to go off, hug the left wall, shoot down, and screw attack the floor to get ET16. After the power bomb goes off, climb into the uncovered morph ball tunnel to get PB16.

Go left to return to the big first room of Sector 3. Make your way to the bottom-right door, shoot the gate and break the floor with speed boost. Plant a power bomb to uncover a path to a hidden room with PB17; this is the only spot in a run where a midair bomb jump is ever useful, as it allows Samus to get into the tunnel before the power bomb is finished (because Samus can't grab ledges while a power bomb is going off).

Go right and fall down the long vertical shaft. Take the bottom-right door, get MT36, keep going right and shoot the gate. Destroy the screw attack blocks at the bottom-right corner of the big heated room, then speed boost through the bottom-right door and shinespark up against the far right wall to shinespark up the tallest vertical shaft in the game, also obtaining PB18. You will pass by PB19 while shinesparking up; just screw attack the ceiling of the alcove by it to get it. Fall back down the long shaft and return to the large heated room. Space jump up to get ET17, and follow the morph ball tunnel to get MT37.

From the heated room, after opening the gate again, start running left. The moment you enter the vertical shaft with the stretchies, shoot the door and space boost through the long heated hall. In the room after the heated hall, plant a power bomb to uncover a maze below leading to PB20. Climb up the stretchy shaft to the very top, take the left door, fall to the room below, and run left into the first big room until you have a shine. Shinespark left through the center left door to shinespark through another long heated hall with sidehoppers.

Enter the door on the left, plant a power bomb, then start running from as far right of the missile tank as possible. Get MT38 while the power bomb goes off, so the wall is destroyed after the acquisition animation. Either speed boost jump into the speed boost blocks at the left side of the room or shinespark up (the former is faster but harder and riskier). Climb up the room to get ET18. Screw attack the floor to find a door leading to the shortcut to sector 5. Before going through the shortcut, screw attack the ceiling by the door and shoot the block to uncover PB21.

Go to Sector 5. Sector 3 should be cleaned up now.

Count: 1899 Energy, 200/195 Missiles, 52/50 Power Bombs

Sector 5 Cleanup

This is the shortest cleanup sector besides Sector 4 (which should be already cleaned up).

Immediately upon entering Sector 5, screw attack through the ceiling and shoot a charged wave shot to open the gate and kill the two pirates. Run left, space jump along the left wall, shoot both gates and then shoot the floor to uncover PB22.

Fall all the way back down, then keep running left until you're at the bottom-left corner of the room that nightmare was roaming around in the background. Space jump up the left side of this room, shoot the top-left door, run left to charge a shine, then shinespark through the door to get MT39 and PB23.

Go back to the bottom-left corner of the room that contained Nightmare, and go to the bottom-left door. Shoot the ceiling and screw attack the bomb block to get MT40. Head left two more rooms and jump through the fake floor below MT41 to get it. Screw attack the blocks on the left to take the shortcut to Sector 6.

Sector 5 should now be cleaned up.

Count: 1899 Energy, 215/210 Missiles, 56/54 Power Bombs

Sector 6 Cleanup

This is the most difficult part of cleanup, and the most difficult part of the 100% category, as doing it optimally requires several difficult time-saving risky space boosts.

Space boost through the screw attack blocks upon entering Sector 6 and go to the middle-left door (the room with the six blue X). Screw attack the center wedge, plant a power bomb to clear the enemies. Stand inside the right door that you came from (but don't go in it), then run left, charging your beam. Space boost through the left door, R shooting it while space boosting. Space boost continuously through the top of the next room, then through all the speed boost blocks in the giant puzzle room in the left to quickly get PB24.

Fall down, run left to give some space, then run right to charge a shine by a slope. Shinespark into the slope then space boost high up to break the speed boost blocks above PB25. Leave the room by space jumping along the right side.

Take the path to the Restricted Sector and speed boost through all of the halls. At the last room, jump while speed boosting into the center of the ceiling, then space jump up to get PB26. Do NOT shinespark directly up or you will be stuck at Sector 1, unable to return quickly. If you want to, you can do a diagonal shinespark.

Leave the restricted sector, and go to the room where you fought BOX 2 and got Wave Beam. Take the door on the right, screw attack the ceiling and plant a power bomb above. While the power bomb is going off, go right and open the gate with wave beam to get MT42. Go back up to where you planted a power bomb to get the most difficult and arbitrary power bomb tank in the game, PB27.

(to do - strats about this power bomb tank)

Go back to the room with the six blue X and screw attack the wedge in the center again. Start running from the left of the wedge and space boost through the wall in the next room. If you can, space boost all the way across this puzzle room to get ET19 very quickly. If space boosting proves to be too difficult, feel free to shinespark instead, but it is slower.

(to do - bomb puzzle here)

After solving the bomb puzzle, either space boost through the left door and through the clutter of speed boost blocks, or shinespark (But shinesparking is several seconds slower). Head for the right door directly above, go through the following room. Plant a power bomb, kill the fake missile tank, and roll through the bottom to get MT43. Sector 6 is now done.

Head in the direction of the recharge room at the start of Sector 6, except instead of going to the recharge room, screw attack the open floor, then screw attack the bottom-left corner to reach the shortcut to Sector 4. In Sector 4, simply fall down the vertical shaft and screw attack the floor to find the shortcut to Sector 2.

Count: 1999 Energy, 225/220 Missiles, 64/62 Power Bombs

Sector 2 Cleanup

Space boost through the screw attack blocks and go above to the room with the Level 1 switch. Screw attack the top-right corner to reach a notorious room named Crumble City. Space jump carefully across Crumble City, to the top-left corner for ET20. Space jump right until you see the gap down, then fall down the gap, and space jump to PB28. You cannot directly fall from a crumble block by ET20 and onto PB28, as if you hit the top crumble blocks, there is floor above PB28 and you have no option except to run left, fall to the bottom, and start over. Leave Crumble City, leave the room with the Level 1 switch, take the bottom-left door, and run through the hall with two ki-hunters.

If you took Route #2, then run to the vine room missile tank on the left side, get the missing missile tank there, take the shortcut to Sector 1 and get the power bomb tank there. Take the shortcut back to Sector 2, using a difficult space boost to reach the initial large sector 2 room again. Both routes should be converged at this point.

Take the blue door on the right side, planting a power bomb as you enter to uncover a path in the right wall to MT44. Go back to the main room, and use the morph ball tunnel at the very bottom right corner. In the next room, screw attack the top right corner, plant a power bomb and get MT45. The power bomb should have cleared the bomb block at the bottom-left corner of the alcove with MT45. Use the tunnel, take the bottom left door, and in the 2nd room, plant another power bomb to clear more bomb blocks. Take the first door on the left you see as you fall down this vertical shaft.

Use two well-timed space jumps after landing on a crumble block to quickly reach PB29. Alternatively, you can use a diffusion missile to freeze the rippers, but it is luck-dependent and slower. Make sure you don't accidentally screw attack the frozen rippers! At where PB29 is, fall down a hidden vertical tunnel and shoot down to uncover PB30. Screw attack the bomb block at the bottom and climb out of this room.

Keep falling down the vertical shaft until the next door on the left. Enter it, space jump over the pond to get MT46. Take the underwater door and use screw attack to quickly get MT47 in the next room. Leave the water room, and take the first already-opened door on the right while climbing up the vertical shaft.

Head right towards where you fought Zazabi. Screw attack the top-right corner to reach a giant room requiring several shinesparks. Complete it to get PB31.

Immediately after getting PB31, pause buffer to try to shine charge in between the two crumble blocks. If done correctly, you have barely enough time to fall down and shinespark for MT48. If you missed it, then charge a shine at the bottom of the room.

Leave via Zazabi's room, and go back through where the SA-X chased you after obtaining Space Jump from Yakuza. You should have every expansion in the game except for one power bomb tank now.

Count: 2099 Energy, 250 Missiles, 72 Power Bombs

Endgame

In the Reactor Room, take the opened door on the top-left corner. Climb out of this room and go through the red door. Take the top-left door in the shaft you climbed at the very beginning of the run, and run left through the following hall. Climb up this shaft, screw attack the power bomb barrier at the top-right corner, and enter the room behind it.

Go to the top right ledge, morph, spring ball, and hold right AFTER the peak of your spring ball to enter the correct hidden morph ball tunnel. Before getting the last PB32, plant a power bomb to clear the block for exiting out of the tunnel.

Before heading for the navigation room, make sure you have every item in the game! Once you enter the navigation room, you cannot enter other sectors until you save and finish the game!

Take the path towards the Operation Deck, as if this were any%. This time, however, you'll have the long conversation with Adam just before the elevator to the Operations Deck. After this conversation, the rest of the run is identical to any%.

Count: 2099 Energy, 250 Missiles, 74 Power Bombs

Alternate Routes

Despite Metroid Fusion's linear item progression, there are alternate routes players can take for 100%.

Minor Cleanup Route

There are two methods of collecting two certain expansions in 100%. Both routes, if fully optimized, are within a half in-game second of each other, and so picking the route completely comes down to personal preference.

The two expansions are the power bomb tank in Sector 1 at the top right corner behind the blue door, and the vine room missile tank below the initial save room of Sector 2.

Route #1

• Collect the vine room missile tank after defeating Nettori, and obtaining Plasma Beam.
• Get the power bomb tank in Sector 1 by the end of Sector 1 cleanup, before going to Sector 3.
• There is no space boosting nor any shinesparks used
• The strat to get the vine room missile tank is tricky, as it requires not killing either of the flying enemies or else the first vine spawns; this slows down Samus when exiting the room as she must jump over the vine instead of run across it. Thus, ice missiles are used to freeze the second vine and both flying enemies to disable them, but not spawn the first vine.
• The power bomb tank is a very annoying detour
• This route is ultimately very slightly faster. The difference is so negligible (less than a half second), however, that it comes down to which route the player do more optimally.

Route #2

• Leave both expansions for Sector 2 Cleanup. After clearing Crumble City, head for the vine room missile tank and get it, then take the shortcut to Sector 1 to get the power bomb tank.
• When returning to Sector 2 via the same shortcut, for this route to be as fast as Route #1, the player must space boost through the vine room and through the door, opening it via R-shooting a charge shot. This is a short yet difficult space boost.
• Cleanup before this part is much smoother, as there are fewer detours, and the detour after Nettori is not needed. Furthermore, while this detour is longer than the detours in Route #1, the player is collecting two expansions in one longer trip.
• This route is ultimately very slightly slower. The difference is so negligible (less than a half second), however, that it comes down to which route the player do more optimally.

Circular Cleanup Routes

In the Metroid Fusion 3D map, the sectors are laid out in a circular fashion. The detailed route above starts in Sector 1, and goes to Sectors 3, 5, 6, 4, 2, and exits via the Reactor. Thus, Samus travels in a counter-clockwise direction around the station. This is called the Counter-Clockwise Cleanup Route.

The old cleanup route went in the opposite direction, starting in Sector 1 and going to Sectors 2, 4, 6, 5, 3, and exits via the navigation room in Sector 3. This is called the Clockwise Cleanup Route. This route is roughly 10 in-game seconds slower than the Counterclockwise route, primarily because there are two elevators Samus takes to the Main Deck, whereas Samus takes the faster Reactor path instead in the Counterclockwise Route.

While the clockwise route is slower, some players may opt for using this route. Most individual room strategies are the same; however, there are slightly different variations on tricks. While a player can use this route if the player likes it more, it is recommended to stick to the counter-clockwise route instead.