List of fanfiction released throughout the 2000s.
- Aaahh!!! Real Monsters: The Movie (Aaahh!!! Real Monsters)
- Aeon Natum Engel (Neon Genesis Evangelion, CthulhuTech, First Encounter Assault Recon)
- All My Kittens (The Aristocats)
- All Things Probable Series (Kim Possible)
- Alone, Together (Kim Possible)
- Alternate Destination (Captain Planet and the Planeteers)
- And If That Don't Work? (Neon Genesis Evangelion, The Spoony Experiment, Team Fortress 2)
- Another Brother (Avatar: The Last Airbender)
- Another Rainbow In Another Sky (My Little Pony 'n Friends)
- Antiphony (Aladdin: The Series)
- Anxiety (NUMB3RS)
- Anything For Charity (NUMB3RS)
- Artemis Fowl and the House Elf (Artemis Fowl, Harry Potter)
- Arc of Sacrifices (Harry Potter)
- Arthur Goes Fourth (Arthur)
- Arthur Grown Up (Arthur)
- Attack Of The 100 Foot Meg Griffin (Family Guy)
- Avatar Aang: An Annotated Bibliography (Avatar: The Last Airbender)
- Avatar: Better World (Avatar: The Last Airbender)
- The Awful Truth About The Powerpuff Girls (The Powerpuff Girls)
- Azula Trilogy (Avatar: The Last Airbender)
- Bad Influence (Jem)
- Bart Simpson: Attorney at Law (The Simpsons)
- Before We Had Wings (Haibane Renmei)
- Best Enemies (Kim Possible)
- Best F(r)iends (Harvest Moon DS)
- Best Kept Secret (Fullmetal Alchemist)
- Better Off Alone (Super Mario Bros.)
- The Biju Biju Fruit (One Piece, Naruto)
- The Black Stallion (My Little Pony)
- Blame It on the Brain (Futurama)
- Blaze of Glory (NUMB3RS)
- Blood Bond, Blood Omen Series (Kim Possible)
- Bloodlines (Naruto)
- Blood, Silk, and Steel (Avatar: The Last Airbender)
- Blooper Mario Sunshine (Super Mario Bros.)
- A Bond of Honor (Kim Possible)
- Bowser's Mexico Adventure (Super Mario Bros.)
- A Boy, a Girl and a Dog: The Leithian Script (The Silmarillion)
- Breaking the Code (NUMB3RS, Foyle's War)
- Burning Black (The Fairly OddParents)
- Most of the stories in the Calvinverse: (Calvin and Hobbes)
- Captain Avatar and the Avateers (Avatar: The Last Airbender Captain Planet and the Planeteers)
- Casey Steele (Whateley Universe)
- Cat Tales (Batman)
- The CATverse (Batman)
- Change of Heart (Super Mario Bros.)
- Chaos and the Aftermath (Metroid)
- Changing Luck (Teen Titans)
- Chasing the Rainbow (My Little Pony)
- Children of an Elder God: Started in 1999, finished in this decade. (Neon Genesis Evangelion/H. P. Lovecraft)
- C Is For Cat Burglar (NUMB3RS)
- Clash's Revolt (Jem)
- Code Geass: Lelouch of Britannia (Code Geass)
- Code Geass Megiddo (Code Geass)
- Cold Nights (Azumanga Daioh)
- Control (Azumanga Daioh)
- The Count's World (Super Paper Mario)
- Coventina's Crown (Sonic the Comic)
- Curses! (Psychonauts)
- D&D Cartoon: Legacy (Dungeons & Dragons)
- Dance with the Demons (Batman)
- Dangerverse (Harry Potter)
- The Dark Lords of Nerima (Ranma ½, Sailor Moon)
- The Darkness of My Heart (Foster's Home for Imaginary Friends)
- The Dark Side of Innocence (Pokémon)
- The Darwin Chronicles (X-Men)
- Deception Unveiled (Jem)
- Descent into Darkness (Sonic the Hedgehog)
- A Different Lesson (Kung Fu Panda)
- A Different Point of View (Arthur)
- Disappearing Doctor (Kim Possible)
- Distorted Reality (Avatar: The Last Airbender)
- Don Eppes (NUMB3RS)
- Dont Stay Away From Home For Too Long (NUMB3RS)
- Ducktales: Twenty Years Later (DuckTales (1987), Darkwing Duck, TaleSpin)
- Dumbledore's Army and the Year of Darkness (Harry Potter)
- The Dream Land Story (Kirby; both versions)
- Ed Abuse (Ed, Edd n Eddy)
- Ed, Edd, Eddy, n Edna (Ed, Edd n Eddy)
- The Ed Edd N Eddy Project (Ed, Edd n Eddy)
- Elemental Four (NUMB3RS)
- Embers (Avatar: The Last Airbender)
- Encryptions (NUMB3RS)
- Enslaved (Avatar: The Last Airbender)
- Eternal (My Little Pony)
- Evangelion 303
- Everybody's Gotta Leave Sometime (Peanuts)
- Face The Strange (Harry Potter, Sonic the Hedgehog, Twilight, Yu Yu Hakusho)
- Facing the Future Series (Danny Phantom)
- Fake (Maria Watches Over Us)
- Father Figure (NUMB3RS)
- Fire! (Marvel Universe)
- The Fall of the Fire Empire (Avatar: The Last Airbender)
- Fallen Angel (Sonic the Hedgehog)
- Fang Vice Addiction (Negima! Magister Negi Magi with a dash of Vampire: The Masquerade)
- Farewell to Life the Way We Knew It (Jem)
- A Few New Tricks (Kim Possible)
- Fighting Chaos (NUMB3RS)
- The Fire Chapters (Avatar: The Last Airbender)
- Fire and Shadow (Warrior Cats)
- Flash by Northwest (DC Animated Universe)
- Flinch (Super Smash Bros. Brawl)
- A Force of Four (Power Girl)
- For Good (Buzz Lightyear of Star Command)
- Forfeit (Ed, Edd n Eddy)
- Frankie Rules (Foster's Home for Imaginary Friends)
- Frenzy (Sonic the Hedgehog)
- Fresh Blood (Jem)
- Frostbitten Flower (Harvest Moon: A Wonderful Life)
- Full Circle (Fullmetal Alchemist)
- Funeral For A Flash (The Flash)
- Galton's Children (Code Geass, Elfen Lied)
- The Games Tent (Aaahh!!! Real Monsters)
- Girl Days (Ranma ½)
- A Goddess Comes to Call (Ah! My Goddess, Bubblegum Crisis)
- The Good Doctor (NCIS)
- Guide Me Home (Avatar: The Last Airbender)
- The Grim Edventures of Ed, Edd n Eddy (Ed, Edd n Eddy The Grim Adventures Of Billyand Mandy)
- A Growing Affection (Naruto)
- Harry Potter and the Methods of Rationality
- Harry Potter and the Mystic Force (Power Rangers Mystic Force, Harry Potter)
- The Heart The Soul (Neon Genesis Evangelion)
- Hearts of Ice: (Ranma ½)
- Hellsister Trilogy (Supergirl)
- Here In My Arms (Rosario + Vampire)
- Here There Be Monsters (Shazam)
- Higher Learning (Neon Genesis Evangelion)
- His and Hers (Danny Phantom)
- Horny Lil' Devils (Kim Possible)
- How Stormer Got Her Groove Back (Jem)
- How to Break a Family (Arthur)
- How To Write ATSS Story (The Secret Show)
- Human After All (Robotboy)
- The Hyde Factor (Kim Possible)
- The Ikaris (Neon Genesis Evangelion)
- I Am Legend (Dream Brother) (NUMB3RS)
- If I'm In Love, PLEASE SHOOT ME! (Camp Lazlo)
- Immortality Syndrome (The Powerpuff Girls)
- In Short Supply (Invader Zim)
- Invader Franny (Invader Zim and Franny K. Stein)
- Invader Zim: The Series (Invader Zim)
- Invisible Sun (FusionFall)
- I Will Remember You (Code Lyoko)
- Jedi Harris (Buffyverse, Star Wars, Stargate-verse, many more)
- Jewel of Darkness (Teen Titans)
- Jordan (NCIS)
- The JWL (Professional Wrestling)
- Kara of Rokyn (Superman)
- The Ketsueki Quadrilogy (Mortal Kombat, Street Fighter, Tekken, Soul Series)
- Kingdom Crossovers (Kingdom Hearts, Invader Zim, Calvin and Hobbes, Planescape: Torment, and many more)
- King of The Hill Episode 1: Peggy's Revenge (King of the Hill)
- Know Thyself (Harry Potter, The Matrix)
- Know Thyself: the Prelude (Harry Potter, The Matrix)
- Kyoshi Revolts (Avatar: The Last Airbender)
- Lab Rat (Danny Phantom)
- Ladder (The Powerpuff Girls)
- The Last Firebender (Avatar: The Last Airbender)
- La Serie De Ken (Pokémon)
- Last Child of Krypton (Neon Genesis Evangelion, Superman)
- The Last Son (Superman/DC Comics, X-Men: Evolution/Marvel)
- The Leap Forward (NUMB3RS, Quantum Leap)
- Legacy of the Red Sun (Star Wars, Superman)
- Let The World Smile (The Legend of Zelda)
- Light of the Snow Red Village
- Lessons from the Mountain (The Silmarillion)
- LMS (Rock Raiders, BIONICLE)
- Lost (Pokémon)
- The Lotus Bloom (Kim Possible)
- Love Ain't Easy, It's Ezzy (Total Drama)
- Lost Storms: Stormy's Forgotten Past (Rainbow Brite)
- Love Hina Double Trouble (Kamen Rider Double, Love Hina)
- Luna's Hubby (Harry Potter)
- Ma'at (Whateley Universe)
- Mado of Stone Mil (Haibane Renmei)
- Manipulation (NUMB3RS)
- Married to the Koopa King (Super Mario Bros.)
- Mai's Ramblings (Avatar: The Last Airbender)
- married to the flames (Avatar: The Last Airbender)
- The Marvelous World Of DC (Marvel Comics, The DCU DC Vertigo, Image Comics, Dark Horse Comics, and Harry Potter)
- Máscara Sonreindo (Lucky Star)
- Maslow (Kim Possible)
- Maternal Instinct (Kim Possible)
- Maybe The Last Archie Story (Archie Comics)
- Meg's Family Series (Family Guy)
- Mended (Pokémon)
- The Merry Go Round Broke Down (Who Framed Roger Rabbit)
- Midnight Savior (Kim Possible)
- Miharu's Story of Star Comand (Buzz Lightyear of Star Command)
- The Misery Senshi Neo Zero Double Blitzkrieg Debacle (Daria, Sailor Moon)
- The Misfits Series (X-Men: Evolution, G.I. Joe: A Real American Hero)
- The earlier stories of The Midnightverse (Chip 'n Dale: Rescue Rangers)
- Morality's Choice (Kim Possible)
- The More Things Change Series (Kim Possible)
- More Than Human (The Powerpuff Girls)
- More Than Meets the Eye (Spider-Man, Transformers)
- More than My Friend (Foster's Home for Imaginary Friends)
- The Myamoto Project (Pokémon)
- My Immortal (Harry Potter)
- My Snow Girl (Rosario + Vampire)
- Nala: My Father's Madness (The Lion King)
- Nature Studies (Discworld)
- The New Captain N (Captain N: The Game Master)
- The New Guild (Discworld)
- Nights in the Big City (Kim Possible)
- Neon Genesis Evangelion: Genocide
- Netherworld Nightmare (Danny Phantom)
- The New Lives Saga (Sailor Moon, Pokémon, Zatch Bell!, One Piece, Ranma ½, Naruto)
- The Next Best Thing to Normal (Batman: The Animated Series)
- Nine Men and a Little Lady (The Lord of the Rings)
- Nobody Dies (Neon Genesis Evangelion)
- Not a Monster (Super Mario Bros.)
- Not Completely, Altogether Here (Wicked)
- Not So Far (NUMB3RS)
- The Nowakverse (Chip 'n Dale: Rescue Rangers)
- Not Quite Heroes (Kim Possible)
- Not So Far (NUMB3RS)
- Numb3rs Ties That Bind (NUMB3RS)
- The Official Fanfiction University of Middle-earth
- Of Love and Bunnies (Power Rangers)
- Of Mice and Mayhem (Chip 'n Dale: Rescue Rangers)
- Of Monsters and Men (Code Geass)
- Once More with Feeling (Neon Genesis Evangelion)
- Onegai, Megami-Sama! (Ah! My Goddess, Please Teacher!)
- The One I Love Is...: (Neon Genesis Evangelion, started in 1999.)
- The Other Side Of Tomorrow (The Adventures of Jimmy Neutron: Boy Genius)
- Origin Story (Buffy the Vampire Slayer, Power Girl)
- Our Time Is Now (Jem)
- Paper Mario: The Temple of the Sun (Super Mario Bros.)
- Paragon (Kim Possible)
- Parentheses: Anti-Fluff Drabble (Ben 10)
- Partially Kissed Hero (Harry Potter)
- A Period of Silence (Kim Possible)
- Phantom's Secret Diary (Danny Phantom)
- Phoenix Rising (Pokémon). Started in 1999.
- Phoenix's Life (Harry Potter)
- Plan 7 of 9 from Outer Space (Star Trek: Voyager)
- The Planets (Fullmetal Alchemist)
- Plight of Persephone (Hercules)
- Pokémon Master: Started in 1999.
- Ports in a Storm (NUMB3RS)
- Possibility Engine (Kim Possible)
- Power Of The Soul (Kingdom Hearts)
- Pretty Cure Perfume Preppy
- Pretty Ore (Harvest Moon: More Friends of Mineral Town)
- Prinzessin (Total Drama)
- The Private Diary of Elizabeth Quatermain (The League of Extraordinary Gentlemen)
- A Prize for Three Empires (Marvel Universe)
- Promises Kept (Wicked)
- Psalm of the Lark (Batman: The Animated Series)
- Q is for Quarry (NUMB3RS)
- Quirk Of Fate (Spider-Man)
- The Rainbow Connection (Rainbow Brite)
- Reconstructed Destinies (Avatar: The Last Airbender)
- Reflections (Tales of the Abyss)
- The Renegades (Kingdom Hearts)
- Respawn of the Dead (Team Fortress 2)
- RE-TAKE (Neon Genesis Evangelion)
- The Return Of Dani Phantom (Danny Phantom)
- REUNION (Kim Possible)
- Revelations of Destiny (Kim Possible)
- Rhyme and Reason (Chip 'n Dale: Rescue Rangers)
- Rise from Darkness (Metroid)
- Risen (X-Men)
- The Road to Shalka
- Rock Stars (Jem)
- The Ronless Factor (Kim Possible)
- RONMAN THE BARBARIAN! (Kim Possible)
- Rosario to Kiva (Kamen Rider Kiva, Rosario + Vampire)
- Sabotage! (Kim Possible)
- Sachiko and Yumi's Alphabet (Maria Watches Over Us)
- Sacrificial Rites (NCIS)
- Scars of War (My Little Pony)
- Scar Tissue (Neon Genesis Evangelion)
- Shadowchasers (Yu-Gi-Oh! 5D's)
- Shadowchasers: City Of Angels (Yu-Gi-Oh! 5D's)
- Shadowchasers: Power Primordial (Yu-Gi-Oh! 5D's)
- The Second Try (Neon Genesis Evangelion)
- Shaggy the Handler (Scooby-Doo)
- Shinji And Warhammer 40 K (Neon Genesis Evangelion, Warhammer 40,000)
- Shinra High SOLDIER (Final Fantasy VII)
- Shinji Ikiryo (Danny Phantom Neon Genesis Evangelion)
- Shinigami Phantom (Danny Phantom Bleach)
- Shiruka yo (Naruto)
- A Simple Wish (Dragon Ball) (Dragon Ball Z)
- The Simpsons Vs Arthur (Arthur, The Simpsons)
- A Small Possibility (Kim Possible)
- Sonic X: Dark Chaos (Sonic X)
- Souls Reborn (Naruto, One Piece)
- Speed and Purpose (Sonic the Comic)
- The Spellbook (Family Guy)
- The Stepbrother Sitch (Kim Possible Phineas and Ferb)
- Spider-X (Spider-Man, X-Men: Evolution)
- Stand Off, or I Knew I Should've Stayed Home Today (NCIS)
- The Subspace Emissary's Worlds Conquest (Super Smash Bros.)
- Superman and Man
- Superman of 2499: The Great Confrontation
- Support (That's So Raven)
- Superwomen of Eva 2: Lone Heir of Krypton
- Sweet Sorrow (Sonic the Hedgehog)
- The Switch Glitch (Fullmetal Alchemist)
- Take Care Bear (Care Bears (1980s))
- Tales of the Otherverse (The DCU, Marvel Universe). Started in 2003.
- Tamers Forever Series (Digimon Tamers)
- Team 8 (Naruto)
- Thawing Permafrost (Rosario + Vampire)
- Those Lacking Spines (Kingdom Hearts)
- Tithing Love (Harvest Moon: More Friends of Mineral Town)
- Thousand Shinji (Neon Genesis Evangelion, Warhammer 40,000)
- Til Death Do Us Part (Pokémon)
- To Catch A Raven (Teen Titans)
- To Face the Wolf (Harry Potter, The Silmarillion)
- Total Alternate Island (Total Drama)
- Total Drama Chris (Total Drama)
- Total Drama Comeback Series (Total Drama)
- Total Sibling Rivalry (Total Drama)
- Touch (Jem)
- The Touch of Green Fire (Kim Possible)
- Transformers Animated: Cybertronian Genesis
- Trial by Tenderness (Ah! My Goddess)
- Triumph of the Retart (Daria, Beavis and Butt-Head, King of the Hill)
- Trusting In Faith (Wicked)
- The Truth Decays (Fullmetal Alchemist, Naruto)
- Tutoring Arnold (Hey Arnold!)
- 24: The Musical
- Twilight Valley (The Land Before Time)
- Twisted Princess (Disney Animated Canon)
- Two Worlds, One Loved One (Darkwing Duck, DuckTales (1987))
- The Vampire of Steel (Buffy the Vampire Slayer, Supergirl)
- Ultimate Misfits (Jem)
- Ultimate Sleepwalker (Sleepwalker)
- Ultimate Spider-Woman (Spider-Man)
- Unacceptable Sitch Series (Kim Possible)
- The Unfantastic Adventures of Bizarro No. 1 (Superman)
- The Unquantifiable Variable (NUMB3RS)
- A Very Kara Christmas (Superman)
- Villain (The Powerpuff Girls'')
- The Violet Room (Kingdom Hearts)
- Walking in the Shadow of Dreams (Neon Genesis Evangelion)
- Wavelet Analysis (NUMB3RS)
- What Insertion? (Slayers, Inuyasha, Detective Conan, Ranma ½, Pokémon)
- When Childhood Ends (Jonny Quest: The Real Adventures)
- When Worlds Collide (Total Drama The Life and Times of Juniper Lee, 6teen, Family Guy, The Simpsons, Danny Phantom, Courage the Cowardly Dog, Kim Possible, Invader Zim, The Grim Adventures of Billy & Mandy, Samurai Jack, South Park, Ed, Edd n Eddy)
- When Worlds Collide Series (Danny Phantom Darkwing Duck)
- Wine Red no Kokoro (Harvest Moon 64)
- Wishing Well (My Little Pony)
- Wolverines, Wendigos and Winchesters (X-Men Film Series, Supernatural)
- Worlds Apart (MLP) (My Little Pony Tales)
- The Worst Possible Sitch (Kim Possible)
- Where the Skeletons Lie (Recess)
- With Apologies to Harlan Ellison (Team Fortress 2)
- With Big Shells and Wings (Super Mario Bros.)
- With this Ring... (Green Lantern) (Green Lantern)
- Wrong Place, Wrong Time (NUMB3RS)
- X-Men 1970
- X-Men: The Early Years
- Yoshi Kart (Massive Multiplayer Crossover)
- Yu-Gi-Oh! Dark Messiah
- Yu-Gi-Oh! The Thousand Year Door
