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Stories with a § in front of them are complete.Stories that look like this have been discontinued.
Font in green is warning or pairings for each story.
Links after the summary are either websites built for that fic or little bits that add to it (maps and timelines).
Harry Potter/Doctor Who Crossovers:
§ Hanging by a Thread
Two men meet after two wars and try to help heal each other.
Harry Potter/9th Doctor
Mostly canon for both series
§ Dust in the Sky
Sequel to Hanging by a Thread. Harry has a life to live now with a wife and children, but he can still find time for the Doctor, no matter what he looks like.
Harry Potter/10th Doctor, hints of canon DW pairings
One, Two, Three, Four, Five, Six
The Future Doesn't Scare Me
Sequel to Dust in the Sky. A series of stories set while Harry works for Torchwood after the 10th Doctor says goodbye.
Harry Potter/Doctor, canon pairings
One, Two
Maps of the Hub: Basement, 1st, & 2nd floors | 3rd & 4th floors (and a really bad sketch of Harry's necklace)
Sequel to Dust in the Sky. Between the Doctor's companions throwing themselves all over him and Harry's life on Earth, their love always manages to bring them together.
Harry Potter/11th Doctor, canon pairings
One, Two, Three
§ Adrenaline Rush
"I can't believe I let you talk me into this."
Doctor/Harry Potter
Crack
§ Freedom and Wonder
The Doctor and Harry stop for a coffee break on an alien space station. (Or, well, as close to coffee as they can find.)
Doctor 10/Harry Potter
§ Giant Snowman
The Doctor suggests a pit stop to celebrate Christmas.
10th Doctor/Harry Potter
§ Give an Ape a Banana
Harry and the Doctor get captured by unfriendly aliens.
Doctor 9/Harry Potter, canon-typical violence
§ Time Storm
The TARDIS gets a bit stuck in the Time/Space Vortex, and Harry and the Doctor take the chance for a break.
Doctor 10/Harry Potter
Harry Potter/Final Fantasy X Crossovers:

Harry Potter defeated Voldemort, but at a price. When a new evil comes that he cannot defeat alone, he and his friends lock themselves in stone to fight it. One day, thousands of years later, Harry is freed and starts a journey with another young man who is equally lost to finish the job Harry once started.
Harry Potter/Tidus
1 - The Beginning, 2 - Ruins, 3 - Besaid & Kilika, 4 - Luca, 5 - Operation Mi'ihen, 6 - Guadosalam, 7 - Macalania & Bevelle, 8 - Calm Lands & Mt. Gagazet, 9 - Zanarkand & Sin, Epilogue

Harry was shunned by his own people because of a bitter vampire and continued living long after England was just a pile of rubble. He watches his world become Spira and finally sets out again to save the world.
Harry Potter/Tidus, some minor Harry Potter/Yuna and Harry Potter/Auron
NOT-SPARKLY-vampire!Harry
1 - Washed Up, 2 - Forgotten Fayth, 3 - The Broken Town, 4 - The Abyss, 5 - Depth, 6 - Ghosts, 7 - Maybes Are Nevers, 8 - Extremes, 9 - Regret, 10 - Fred, 11 - Vampyre, 12 - Blood
Harry Potter/Radiata Stories Crossovers:
§ Fallen Night
Harry slipped when he was standing a little too close, and the next thing he knew, he was far away from everything he'd ever known, with something like eternity waiting for him.
Harry Potter/Jack Russell
Non-human arc, war
Pro - Falling, 1 - Elves, 2 - Humans, 3 - Let It Go, 4 - And If It Returns, 5 - It Was Meant To Be, 6 - Ways of the Dragon, 7 - To Build an Army, 8 - Power Over Life, 9 - Arbitrator, 10 - Blood-Filled Days, 11 - Hic Sunt Dracones
Harry Potter/D.N. Angel Crossovers:
Three years after Dark left, Daisuke, Satoshi, and the Harada sisters find themselves in a far away land, in a far away castle, where enemies are lovers and nothing is as it seems.
Tom Riddle/Harry Potter, Niwa Daisuke/Hiwatari Satoshi, others
1 - The Mysteries of Hogwarts, 2 - Not So Clear As Mud, 3 - DARKKRAD, 4 - What It Is To Be Wanted
Marvel Cinematic Universe/Almost Human Crossovers:
§ Learning How to Trust
Loki is one of the best burglars-for-hire in the whole of the city, able to keep even the cop who's always got an eye on him from knowing when he's up to no good. But when he meets the gorgeous Thor, a pleasure bot, he leaves all of that behind for a slightly more respectable past time.
Loki/Thor
Crossover, Human/Android AU, sexbots, burglary, prostitution, Loki does what he wants, rough sex, questionable consent
Marvel Cinematic Universe/Disney's Frozen Crossovers:
§ Þetta er nóg
Banished to Earth in hopes that he might learn the same lesson Thor had, Loki meets Queen Elsa of Arendelle. But how can two creatures of ice possibly hope to warm the other's heart?
Loki/Elsa
Hurt/comfort, AU, Jötunn!Loki, Loki is a little shit
Fullmetal Alchemist: Chaptered Fanfiction & Series ||| One-Shots & Drabbles
Video Games Series Fanfiction (Non-Crossover)
Anime Series Fanfiction (Non-Crossover)
TV Show & Films Series Fanfiction (Non-Crossover)
Marvel Series Fanfiction (Non-Crossover)
Real Person Fanfiction
Original Fiction
List of Translated Fanfiction
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