Ability route by shirokirby, detailed Code Cube locations are by Woutt64 and me.
Basic Info: CC = Code Cube. You need a certain amount of them in each world to progress. The abilities below the level numbers are what you'll be using for the entirety of that level unless noted otherwise. Arrows indicate that you have to switch to a different ability, the one it's pointing to.
Time starts on selecting story mode in a new file.
1-1 Cutter When Clanky Woods starts chasing you, attack it until it drops a rare golden sticker. Get the sticker and proceed. CC(1) Can't miss it
1-2 Cutter → Fire Robobot CC(1) In the giant can, can't miss it
1-3 Fire Robobot CC(1) Use electric can to swap the Gordo (spike ball with eyes) for the CC.
1-4 Fire Invincible Candy CC(2) To the right of the candy
Clanky Woods (4 CC needed) Fire → Cutter
2-1 Cutter → Jet
2-2 Robobot (Jet) CC(1) In front of a bus at the bottom left during the autoscroller CC(2) Can't miss it CC(3) Can't miss it
2-3 Jet CC(3) Pull lever to unlock
2-4 Jet CC(2) On the roulette table, under one of the yellow balls
Holo Defense API (5 CC needed) Jet
3-1 Jet CC(1) Take upper path and break blocks
3-2 Jet CC(1) In the background of the first Wheel Robobot section CC(2) Enter the orange door and follow the path CC(3) Jump right before reaching the end, follow the path with stars
3-3 Jet CC(3) Press the 2nd switch at the end of the final autoscroller
3-4 Jet Invincible Candy CC(1) At the end of the candy room, go down at the door
3-5 Jet → Hammer
Susie (6 CC needed) Hammer
4-1 Hammer → Fire Robobot CC(3) Punch the roller into the yellow blocks
4-2 Fire CC(1) Between 2 platforms, can't miss it CC(2) In extra room, break bomb blocks to unlock chest Robobot Parasol (Bot) CC(3) Blow away poison gas with parasol Robobot
4-3 Fire (Jet)
4-4 Fire (Jet) CC(1) Between 2 lasers, can't miss it CC(3) Fire switch
4-5 Fire (Jet)
Mecha Knight (6 CC needed) Fire (Jet) → Ninja
5-1 Ninja → Jet CC(2) Open a chest between 2 music note springs
5-2 Jet CC(1) Grab the battery from Carry Dee CC(2) On the roulette table, can't miss it Robobot CC(3) Punch the giant pool ball into the yellow blocks
5-3 Jet CC(3) Press the 4th switch to unlock the chest
5-4 Jet → Cutter Robobot Wheel (Bot) CC(2) Go fast enough in the left-right section CC(3) Right before the goal, can't miss it
5-5 Cutter
Dedede Clone (7 CC needed) Cutter
6-1 Cutter CC(1) Hit switch to lower chest Candy
6-2 Cutter CC(2) Carry the battery to the pod CC(3) Press all switches to unlock lower path in background
6-3 Cutter Robobot
6-4 Cutter → Fire → Jet CC(2) In the dodge background section, can't miss it CC(3) Go to the left in the vertical room where there's a small left path
6-5 Jet Robobot Spark (Bot) CC(1) Drop the carryable block onto the yellow blocks Jet (Bot) CC(3) Hit all the switches in section with minibosses and stay at the bottom of the screen Robobot Spark (Bot)
Mecha Knight+ and President Haltmann (7 CC needed) There's three fast strats you can do here; using Doctor, Hammer or Cutter. Use whatever you've practiced the most.
World 7 [Mind in the Program]
Star Dream:
Phase 1 Max charge attack before it uses the heart shields, otherwise try to finish before it does the meteor storm attack.
Phase 2 Save the max charge attack for when it's at half health left.
Phase 3 Should finish around when the big 1 appears; assuming you have enough health left, just tank the damage from the big numbers and keep shooting. Gather charge from destroying the objects and spam charge attacks.
Phase 4 hardest part of the run
Time ends on the final circle pad/d-pad input.