Some games are ridiculously convoluted so here's a full walkthrough to help you complete Mystik Belle's complex journey.
Before we begin, click here for the full 100% completed Mystik Belle world map. The following guide features handy numbers so that you can make note of the step that you're on whenever you want to quit playing. By the way, I played through the PlayStation 4 version so if you're playing another version then the controls may be different. Anyway, let's get this started!
 First, the controls. You push X to jump, Square to attack, Triangle to pick items up, and Circle to open the items menu.  Pick up the Hall Pass (which looks like an apple) and use it via the item menu on the guard to the right.  Go all the way right, all the way down, right, up, and right to see Ms. Willow stirring a cauldron. Pick up the Empty Spray Pump to her right.  Head back to left of the teleportation room then up and right. Use the Empty Spray Pump on the tank then pick up the Toxic Weedkiller.  Head back to the right of the teleportation room then down. Pick up the Rubbish at the bottom.  Go right and use the Toxic Weedkiller in front of the Carnivorous Plant to kill it then pick up the Stinky Leaf. (Unlocks "Herbicidal Tendencies" trophy / achievement)  Head left through the newly uncovered doorway and you'll see Nicky reading a book. Go left from here then down then left through an enemy-filled hallway. Past this hallway, head up a couple of blocks and enter the room to your left then collect the Flimsy Chain from the toilet.  Exit the room and head up and to the left to see Ms. Bitterwarts in the kitchen. Go left and down. Pick up the Sharp Glass then throw the Rubbish, Sharp Glass, and Stinky Leaf into the dumpster. Pick up the resulting Fly Magnet.  Head all the way left, up, then right. Be careful to stun the giant frogs as they will eat your precious flies. After the frog room, hop to the roof on the right to pick up the Durable Crowbar.  Hop down and go right back to Ms. Bitterwarts. If you have enough flies left, use the Fly Magnet on her then pick up the Smelly Fish Head and some Shiny Copper Foil.  Run all the way back to the left and use the Durable Crowbar on the hatch. Go down and to the right. Deposit the Metal Scrap and Smelly Fish Head into the chest.
 Go all the way right and pick up the Sharp Saw. You can talk to Franky, too.  Head back left then all the way up then right past the frog room. Carefully jump up the platforms and head to the upper-left room. Pick up the Glass Jar and keep moving left.  In this room, drop the Hall Pass on the right-hand side of the floor. Jump up to the platform and wait for the Hermit Lizard to be fooled by the "apple" then jump on the lizard and retrieve its Sturdy Box as well as your dropped Hall Pass.  Deposit the Sturdy Box into the chest then head right and down until you reach a bent curtain rod that you may have spotted earlier. Use the Sharp Saw on it then pick up the Brass Rod. Go up and right to deposit the Flimsy Saw into the chest.  Go left, up the column, and right to see Ms. Willow's kitty Midnight. In the next room, destroy all the flying books and one will drop the Scientific Tome. Obviously, pick it up!  Head to the right of this room and shoot above the wooden door to open a shortcut. Go through it, run right, go down, and left then give the Scientific Tome to Nicky. Drop the Brass Rod on the ground then pick it up again to spawn A Leyden Jar! Pick it up, of course. (Unlocks "Clever Clogs" trophy / achievement)  Reclaim the Flimsy Saw from the chest in this room. Go left, up, and right to visit Midnight (the cat) again. Use the Leyden Jar on it then collect the Charged Jar!  Run right, ensure your health is full and use the teleporter to go to the leftmost point. From there, go right then use the Charged Jar on Franky to trigger the first boss fight!  This boss is pretty easy. Just keep jumping and shooting at its head. You'll receive the Lightning Spell for your troubles. To use it, hold the attack button.
 After the boss fight, talk to Franky to obtain the Sledgehammer. Then, use the Lightning Spell above the door to the left and exit the room.  Go left, all the way up, right, up using the platforms, and left. You can kill the knight now with one simple Lightning Spell attack. Keep slaying these enemies to reach level 5.  Once you're satisfied, head left and unleash a Lightning Spell on the elevator to move it up and face the second boss; A Science Ninja.  This guy is a bit tougher as he warps around but keep unleashing a fury of spells and melee attacks and he'll eventually go down. You'll acquire the Dash Spell that you can use with the L2 button.  Upon defeating the Science Ninja, pick up Some Copper Wire. At the bottom of this room, store the Copper Wire in the chest and take the Metal Scrap from it.  Run all the way right and down back to the first teleportation room. Go right, down, and right then use the Flimsy Saw on the mop. Pick up the Orange Mop Head. Interact with the bucket a couple times then collect the Old Bucket.  Move right and ignore the Nail Clippers then use the Sledgehammer on the mechanism to lower the drawbridge.
 Keep moving right then use all three metal scraps on the metal hopper.  Backtrack left, shoot the Horseshoe then pick it up, and collect the Nail Clippers that we walked by earlier.  Head right and interact with the chest to store the Nail Clippers, Horseshoe, and Old Bucket. Retrieve the Sturdy Box and Smelly Fish Head.  Walk left and use the Sturdy Box on the sandbox then pick up the Box Full of Sand.  Go left past the room that Nicky used to be in, down, and left all the way until you see a bald lady named Romana. Give her the Orange Mop Head then pick up the Wooden Gear Part.  Move all the way right to Detention Dungeon and keep running right and down. Hop on the platform then pick up the Skull in the bottom-right corner of the room.  In this same room, work your way to the upper-right corner. Shoot the eye above the door in the next room with a Lightning Spell. In the next room, go all the way to the bottom. Move left, hop on a bucket, and enter the top-left room. Keep going left, kill the tough reaper, and pick up the Screw-in Hook at the bottom-left of the room. Phew!  Head left and when you reach a pile of bones with a sign in the middle, use the Smelly Fish Head. Jump on the worm and ride it. Hop off onto a ledge next to a platform with four spikes on it. Jump and Dash Spell to the right then pick up the Can of Gear Oil.  Ride the worm again and get off on the same platform as before. Jump and Dash Spell continuously to the left. Head all the way down and go right. Deposit the Can of Gear Oil and Screw-in Hook in the chest. Go back left and up then pick up the Pile of Bones.  Go back to the teleportation room and teleport to the left point. Head left, up a bit, and right then use the Pile of Bones and Skull on the dumpster. Teleport back to the bottom point.
 Head all the way right, examine the garbage can, pick up the Wooden Gear Part that spawns then collect the Gear Mold.  Teleport to the right point, run all the way right and use the Gear Mold on the metal hopper. Hop on the bellows to the right a bunch then interact with the chain. Collect the Large Gear that emerges as well as the Sturdy Box that's in front of the fire pit. (Unlocks "Belle?! BELLE!" trophy / achievement)  Teleport to the bottom point and reclaim the Horseshoe and Can of Gear Oil. Go right and use the Large Gear and Can of Gear Oil on the mechanism. Interact with it and Professor Sinclair will transform into a werewolf.  This boss fight is easy. Use Dash Spell to avoid its attacks and Lightning Spell on its head. You'll earn the Double-Jump Spell once he's down.
 Go left from the boss room and collect Some Copper Wire from the chest. Head left, up, and left. Interact with the broken wires underneath the platform then walk away and you'll automatically put an Electric Magnet on the platform.  Hop on the platform and use a Lightning Spell on the orb. Jump off the platform and collect the Boltcutters. (Unlocks "Scary Fishing" trophy / achievement)  Head left and go all the way up then make a shortcut by opening the door to your right. Run all the way back to the werewolf boss room and use the Boltcutters to cut its nails then collect the Werewolf's Claw.  Teleport to the right point then go right, up, and right and give the Werewolf's Claw to Ms. Willow. Go left, descend to the bottom of the column, then run all the way directly left to face yet another boss!  This boss is super-easy as killing its minions will drop health pick-ups. Anyway, just stay right and keep firing a fury of fireballs and Lightning Spells. You'll receive a Transformation Spell.  Go left and pick up the Sack of Flour. Interact with the mouse hole to the left and head right as a mouse to step on a switch and open the door.  Move right, down, and all the way left then enter the mouse hole to the left of mop-head Romana. Collect the first Piece of Lore. (Unlocks "Star Pupil" trophy / achievement)  Run all the way right, head down and to the left. In this room, enter the mouse hole and pick up the Flower Pot. Go left and get the second Piece of Lore.  Head down and move right to the bucket room. Enter the water and collect the Gardening Trowel then swim back up; quick!  Go up, all the way left, down, and right then teleport to the right point. Head all the way right back to the village. Enter the mouse hole in the far right house and collect the Green Orb. Exit and deposit the Green Orb in the chest to the left.
 Move right and collect a Clump of Grass. Go right and down. Be careful around the raccoons here as they may steal your items! Pick up the Pinecone to the right.  Exit through the top-right of this room then head up and right. In this larger room, jump up and go to the top-right. Fall down from the rightmost platform plant to land on a ledge then jump and keep dashing left to get the third Piece of Lore.  Work your way back to the plant that you fell from and head to the top-right then teleport to the middle point. Exchange the Sack of Flour for the Old Bucket at the chest. Head right to the bridge and dive in the water. Immediately come back up to automatically get a Bucket of Water.  Teleport back to the rightmost point, go right, use the Bucket of Water on the dried-up plant then use the Gardening Trowel and the Flower Pot. Pick up the resulting Bloom of Twilight and prepare for another boss!  This tree is easy as long as you defeat the enemies that it spawns and keep shooting lightning at its face. You'll learn the Bubble Spell after it falls.
 Teleport back to the middle point, head right, up, and right and give Ms. Willow the Bloom of Twilight. Go back to the warp room then head left, up a little, and left. Collect the fourth Piece of Lore in the top-left corner of the room.  Go right, up, and right then enter the mouse hole and press the switch. Fall down the created hole to receive the Bag of Fertilizer.  Head back to the nearby teleportation room and warp to the leftmost point. Go left, up a bit, and right then deposit the Pinecone and Clump of Grass. (Unlocks "Environmentalist" trophy / achievement)  Ascend via the elevator and go all the way up and left. Drop the Sturdy Box in front of the lizard and jump on the platform then it'll climb into it again. (Unlocks "Kind Soul" trophy / achievement)  Go back right then jump to the tricky-to-reach ledge to the right of the moving platforms. Interact with the rope then collect the Thick Rope.  From here, go right, up, right. In this dorm room, head to the top-left and enter the mouse hole to collect the Tarnished Key.
 Exit the room then go down and all the way right. Head down and to the right to enter the warp room. Use the chest to deposit the Old Bucket and take the Green Orb and Screw-in Hook.  Keep going right then jump into the water to the right of the bridge. Go all the way down then take a left. Use the Tarnished Key on the treasure chest and collect the Red Orb.  Head all the way back and surface to the right of the bridge. Go right to the room with the raccoons then take a left at the bottom of it. Keep going down and left and collect the fifth Piece of Lore on the left-hand side of the second underwater room.  Enter the left room and open a shortcut at the end of it. Go directly right and use the Screw-in Hook and the Thick Rope on the big rock.  Go down, kill the giant squid, and head up on the right-hand side of this room. Exit this next room to the right then go back to it and defeat the demon girl. Repeat this again and again and she'll eventually drop a Glowing Amulet. Collect it.  Note: if you travel to a warp point a certain number of times with the Glowing Amulet; you may end up in the World of Obsolete Assets. Scroll down to see the guide for that area.
 Past the teleportation room to the right, place the Red Orb and Green Orb into the left and middle parts of the elevator. Keep going right and up then you'll run into a giant skeleton. Kill it and pick up the Blue Orb.  Trek all the way back to the elevator and place the Blue Orb in the right spot. Take it down and go to the right then interact with the collapsed rocks.  Go left, up, and left then teleport to the bottom-left point. Run all the way right and talk to Professor Sinclair. Pick up the Empty Vial.  Head left and use the chest to reclaim the Sack of Flour. Teleport to the bottom-right point. Go right a bit then drop the Empty Vial under some dripping acid then collect it again to receive the Sulfuric Acid.  Warp to the leftmost point then head left, up, then all the way right and up back to the dorm room. Here, examine a drawer in the top-left of the room then pick up the Paper Tube.  Teleport to the bottom-left point again, head right, and give the Paper Tube, Sulfuric Acid, Sack of Flour, and Bag of Fertilizer to Professor Sinclair. Pick up the Stick of Dynamite.  Warp to the bottom-right point and head to the collapsed rocks to the right again. Now, use the Stick of Dynamite on the rocks, shoot a fireball at it and back away. (Unlocks "Boom Goes the Dynamite!" trophy / achievement)  Collect the Dragon Scale to the right then head back up the elevator and fight a giant spider boss!  Again, it's easy as long as you kill its minions and keep shooting lightning at its head. You'll learn the Brick-Breaker Spell once it's defeated.  Head all the way directly right from here then use the Brick-Breaker Spell on the wall and collect the sixth Piece of Lore.
 Go back to the teleportation room and warp to the central point. Head up and right and give the Dragon Scale to Ms. Willow. Pick up the Mysterious Brew. (Unlocks "Taker of Things" trophy / achievement)  Travel all the way left and down to the bottom-left part of the map with a door leading to an unvisited room. Break down the wall then enter the room and a scene will play. (Unlocks "What Did I Miss?!" trophy / achievement as well as the "Respect My Authority!" and "Speedrunner" trophies / achievements if you managed to fulfill their conditions)  Load up your save then travel all the way up to the unexplored top part of the map. Here, use your Brick-Breaker Spell to progress and receive the seventh Piece of Lore.  Head back, all the way down, then go left. Stand on the leftmost moving platform, jump to the right, and uncover the eighth and final Piece of Lore!  Finally, go back to where you got the first ending. This time, you'll have to actually fight a boss. Hold left to avoid attacks and push X and Square to perform a couple different punches. (Unlocks "Sleepy Girl" trophy / achievement)
World of Obsolete Assets
 As mentioned above, keep warping around with the Glowing Amulet and you'll eventually arrive here. (Unlocks "I Don't Even!" trophy / achievement)  Go left and fight a giant slime boss. Defeat it by unleashing plenty of fireballs and dashing to avoid its attacks. The Lightning Spell does not work. You'll receive the Heal Spell once it's defeated which slowly restores Belle's health. Yay!  Now, you can explore this area to uncover the map and also unlock a shortcut if you want.
Well, there you have it; consider Mystik Belle completed! Good luck getting that precious Speedrunner trophy for beating the whole thing in under an hour. If you have any feedback or questions then feel free to leave a comment below and I'll get back to you ASAP. Please also include the step number if you're referring to a particular step so that I can know exactly where you are in the guide.