Here is a checklist to help you keep track of what guide missions you've already done. Especially helpful if you've been switching guides. I made this list from the list on the FusionFall Wiki, and decided to share it here in case anyone else would find it useful. Just print it out and mark off each mission as you do them. Use the Wiki missions list to check where each character is if you don't know. If you're not sure which missions you've already done you can check by going to your journal and clicking the completed missions tab.
(If you like this page you can repay me in-game. Click here to see how.)
Level 1 - 2x4 Technology - Numbah Two
Level 2 - Haste Makes Paste - Eddy
Level 3 - Into the Vortex - Eduardo
Level 3 - Bring Me the Head of Larry 3000 - Mandark
Level 4 - Time To Go - Numbah Two
Level 4 - Gear Up - Numbuh Two
Level 4 - Terrafuser Tango - Numbuh Two
Level 5 - Pesky Problems - Numbuh Two
Level 5 - Follow Your Node - Numbuh Two
Level 5 - Hide and Go Eek - Numbuh Two
Level 6 - Pokey Punch-Out - Numbuh Two
Level 6 - Bugs And Earplugs - Numbuh Two
Level 8 - Base Case, Part One - Numbuh Two
Level 9 - Base Case, Part Two - Numbuh Two
Level 10 - Major Miner - Numbuh Two
Level 11 - Nuclear Haste - Numbuh Two
Level 12 - Tree House Trouble - Numbuh Two
Level 13 - Max Marathon - Numbuh 311
Level 14 - High Jinx - Grandpa Max
Level 15 - You Make the Call - Grandpa Max
Level 16 - Free Launch - Grandpa Max
Level 17 - Omnitrix Fix - Grandpa Max
Level 18 - Hard Cell - Grandpa Max
Level 19 - Appetite For Destruction - Grandpa Max
Level 20 - No Ghosts Allowed - Grandpa Max
Level 21 - Vine Time - Grandpa Max
Level 22 - Do Not Enter - Grandpa Max
Level 23 - Nowhere To Go - Ben
Level 24 - Tough Cell - Ben
Level 25 - Into The Wild - Hoss Delgado
Level 26 - Chicken Scrap - Hoss Delgado
Level 27 - Mountain Madness - Ben
Level 28 - Dark Times - Hoss Delgado
Level 29 - Sinister Plans - Hoss Delgado
Level 30 - Pit Stop - Hoss Delgado
Level 31 - Bash Your Brains - Hoss Delgado
Level 32 - Welcome to Braintree - Hoss Delgado
Level 33 - Satellite Mission - Hoss Delgado
Level 34 - Captain's Log - Hoss Delgado
Level 35 - Eyebore Easily - Hoss Delgado
Level 36 - Fusion Finale - Hoss Delgado
Level 4 - Blossom Battle - Blossom
Level 4 - Major Worry - Blossom
Level 5 - Sector Defender - Blossom
Level 5 - Lab Assistance - Blossom
Level 6 - Home Invaders - Blossom
Level 6 - Hardware Help - Blossom
Level 7 - Supplies Party - Blossom
Level 8 - Spooky Spies - Blossom
Level 9 - Remember Buttercup - Blossom
Level 10 - Bad Nukes - Blossom
Level 11 - Relay Race - Blossom
Level 12 - See Ya Later, Alternator - Blossom
Level 13 - Dexlabs Delivery - Dexbot
Level 14 - Ms. Missing - Dexbot
Level 15 - Don't Lose Your Head I - Grim
Level 16 - Don't Lose Your Head II - Grim
Level 17 - Laser Blast - Grim
Level 18 - Don't Lose Your Head III - Grim
Level 19 - Love and Hades - Grim
Level 20 - What The Hades - Grim
Level 21 - Strike A Cord - Grim
Level 22 - Power Up - Grim
Level 23 - Spa Daze - Grim
Level 24 - Tracking Jack - Dexter
Level 25 - Warrior's Welcome - Samurai Jack
Level 26 - Magical Aid - Samurai Jack
Level 27 - Tech Meets Magic - Samurai Jack
Level 28 - Horrordactyl Hunt - Samurai Jack
Level 29 - Friend in Need - Samurai Jack
Level 30 - The Power of Bonk - Samurai Jack
Level 31 - Demongone - Samurai Jack
Level 32 - Bully the Bullies - Samurai Jack
Level 33 - Soul Recovery - Samurai Jack
Level 34 - Warriors Reborn - Samurai Jack
Level 35 - The Dark Wizard - Dexter Tech
Level 36 - Shadows of Aku - Samurai Jack
Level 4 - Don't Be a Drip - Ranger Ralphie
Level 4 - Ed-vanced Combat - Ranger Ralphie
Level 5 - Chairman of the Cardboard - Ranger Ralphie
Level 5 - Map Quest - Edd
Level 6 - Crazy Brain Drain - Edd
Level 6 - Treasure Hunt - Edd
Level 7 - Spex Trek - Billy
Level 8 - Sweet and Buried - Billy
Level 9 - Booger Boogie - Billy
Level 10 - Candygram Jam - Billy
Level 11 - Tangelo Fellow - Billy
Level 12 - Kibbles 'n' Hits - Billy
Level 13 - You and Bloo - Bloo
Level 14 - Fun and Games, Part One - Bloo
Level 15 - Fun and Games, Part Two - Bloo
Level 16 - We Deliver - Bloo
Level 17 - Skate Switcheroo - Bloo
Level 18 - Sandy Candy - Bloo
Level 19 - Bloo Is Green - Bloo
Level 20 - Spy Games - Bloo
Level 21 - Tree Treasure - Bloo
Level 22 - Candy Crush - Bloo
Level 22 - Fusion Cuisine - Bloo
Level 24 - Spaced Out - Bloo
Level 25 - Nowhere Dog - Courage
Level 26 - Eggplant Peril - Courage
Level 27 - Slippery Foes - Courage
Level 28 - Valley Ghouls - Courage
Level 29 - Candy Scare - Courage
Level 30 - Monster Mash - Courage
Level 31 - Root of Evil - Courage
Level 32 - Swarm Reception - Courage
Level 33 - Plant Plan - Courage
Level 34 - Shell Game - Samurai Jack
Level 35 - Sap Attack - Samurai Jack
Level 36 - Candy No More - Samurai Jack
Level 4 - Kids Wanted - Jibba Jabba
Level 4 - Poster Imposter - Jibba Jabba
Level 5 - First Matey - Jibba Jabba
Level 5 - Me and Him - Father
Level 5 - Under Development - Father
Level 6 - Gun Run - Father
Level 7 - Wing And A Prayer - Father
Level 8 - Blood Feud - Father
Level 9 - Sweet Recovery - Father
Level 10 - Chemical Xcursion - Father
Level 11 - Say Cheese - Father
Level 12 - Monkey Business - Father
Level 13 - A Boy Named Sue - Ramma Jamma
Level 14 - Not-So-Secret Admirer - Mandroid M-99
Level 15 - Invention Protection, Part One - Mandroid M-99
Level 16 - Invention Protection, Part Two - Mandroid M-99
Level 17 - Wharf War - Mandroid M-99
Level 18 - Beach Boom - Mandroid M-99
Level 19 - Guilt Trip - Mojo Jojo
Level 20 - Panicked Attack - Mojo Jojo
Level 21 - Arboretum Beat 'Em Up - Mojo Jojo
Level 22 - Tech Squares - Mojo Jojo
Level 23 - Chemical Xpert - Mojo Jojo
Level 24 - Princess Pal - Mojo Jojo
Level 25 - Fuzzy Wuzzy - Fuzzy Lumkins
Level 26 - Water You Doing? - Mandy
Level 27 - Post Hypnotic Infection - Mandy
Level 28 - Monkey Shines - Mandy
Level 29 - All Systems Go, Mojo - Mandy
Level 30 - Double Doublecross - Mojo Jojo
Level 31 - Know Your Roots - Mandy
Level 32 - Tree Trapped - Mandy
Level 33 - The Lair Out There - Mandy
Level 34 - Move Over, Mandy - Mandy
Level 35 - Prince Charming - Mandy
Level 36 - The Cracks of Fuse - Mandy