''[[http://www.fimfiction.net/story/149050/a-new-world-a-new-way A New World, A New Way]]'' by zeusdemigod131. [[http://tvtropes.org/pmwiki/pmwiki.php/Fanfic/ANewWorldANewWay Tvtropes page]]
* Recommended by tdntv
* ''Status'': Ongoing
* ''Synopsis'': Arceus has been imprisoned for many millennia, and in that time he has watched his world fall apart. But once he is finally freed from his prison he decides that to protect his Pokémon, and his family, that he will move the Pokémon, and a few select 'humans' to a world where they might live in peace, Equestria. However, not everyone on this new world shares his view of peace and the very presence of the Pokémon upsests some of the citizens of the world, even some of the ones he brought with aren't too happy with the situation. But a god's will is a strong thing and without his willingness the Pokémon and the citizens of Equestria are going to have to learn to get along, or at least tolerate each other. And there's a slight problem with some of the humans too, well, former humans that is.
* ''Comments'': An enjoyable story that combines the worlds of ''{{Franchise/Pokemon}}'' and ''WesternAnimation/MyLittlePonyFriendshipIsMagic'', made even more interesting with touches of concepts like InterspeciesRomance, and the general chaos that is inadvertadely caused by a god who has a bad habit of [[DidntThinkThisThrough not thinking things through]], as well as the trials both worlds face as they try to learn to co-exist.

''[[http://board8.wikia.com/wiki/Doctor_Doom_travels_through_Kanto_with_a_Magikarp_as_his_starter Doctor Doom travels through Kanto with a Magikarp as his starter]]'' by Sir Chris (Less Up-to-Date Alternate Fanfiction.net link [[http://www.fanfiction.net/s/6803324/1/ here]]).
* Recommended by @/{{Igordebraga}} and Navllyk
* ''Status'': Ongoing
* ''Synopsis:'' Doctor Doom got tired of ruling over [[MarvelUniverse his own world]] so he decided that becoming a Pokemon Master would be a good way to spend a week or two. Hilarity (and slaughter) ensues.
* ''Comments:'' Worlds colliding in this hilarious parody. It might not be for the most sensitive (or Pokémon purists) due to its plentiful violence, since no one stands on the path of '''DOOM'''!
[=[[reviews:Doctor Doom travels through Kanto with a Magikarp as his starter]]=]

[[http://feriowind.tumblr.com/tagged/Pokevengers Pokevengers]] by Feriowind
* Recommended by: SAMAS
* Synopsis: What kind of Pokemon would [[Franchise/MarvelCinematicUniverse The Avengers]] have? This isn't simply handing over a random selection of monsters, these pictures represent a look at how these heroes' lives have been shaped by their companions. Tony's Ninetales once belonged to his father, and he wrote the code for Porygon. Captain America fought with a Growlithe by his side, and reunites with him again decades later as an Arcanine. Bruce Banner's Pokemon help keep him and the Hulk calm, and Natasha's Pokemon are [[PetTheDog the few bright spots]] on her black ledger. And how the hell did Nick Fury get ''Mewtwo'' on his team?

''[[Fanfic/APonyOutOfPlace A Pony Out of Place]]'' by [[https://www.fimfiction.net/user/Ausbrony Ausbrony]]
* Recommended by Tropers/ClatoLawa
* Synopsis: When Dialga and Palkia start to attack one another in Alamos Town, a Ponyta named Flare Blitz is caught in the crossfire. After falling into the dimensional rift, he finds himself in [[WesternAnimation/MyLittlePonyFriendshipIsMagic a strange new land filled with brightly coloured ponies]]. Flare doesn't know how he got here or if he can even get back home... The question is, will he even want to go home?

''[[http://www.fanfiction.net/s/5316010/1/Poketroid Poketroid]]'' by [[http://www.fanfiction.net/u/2051974/Gengario Gengario]]
* Recommended by Tropers/PinkCelebi
* Synopsis: "A Pokemon trainer's journey and a bounty hunter's mission become intertwined when the planet Pocket finds itself in danger. But as it turns out, the danger may extend beyond Pocket itself..."

[[http://www.fanfiction.net/s/6869590/1/Complex Complex]] by [[http://www.fanfiction.net/u/922226/MasterShaper MasterShaper]]
* Recommended by {{Tropers/PKMN37}}
* ''Synopsis'': Wanting to put a stop to abuse done to pokemon by abusive trainers, a secret meeting is held by the Elite Four with Datamon. A deal is made to help them in exchange for letting him and his cohorts take over the Pokemon world. They cross over and the Digimon put their world into martial law. Pokemon Training is outlawed and battles are forbidden. Only the officials are allowed to train them. The story then follows a guy who signs up and works under a fun, eccentric man in the military. He gets assigned a Shellder and they work together to solve the strange mysteries around their workplace, which results with them getting into some big trouble.

''[[http://www.fanfiction.net/s/5910693/ Pokemon: Lelouch of the Rebellion]]'' by [[http://www.fanfiction.net/u/1963774/SamJaz SamJaz]]
* Recommended by NG14916
* ''Synopsis'': In a world without mecha, a pokémon trainer named Lelouch Lamperouge attained the power of kings and led a rebellion against the Britannian Empire. This is the story of the boy as he became a man. This is how he became Lelouch of the Revolution.

''[[https://www.fanfiction.net/s/9305868/1/Harry-Potter-and-the-Master-s-Ball Harry Potter and the Master's Ball]]'' by [[https://www.fanfiction.net/u/464973/Mr-Chaos Mr Chaos]]
* Recommended by Tropers/ClatoLawa, {{Tropers/auroVee}}
* FusionFic Crossover with ''Literature/HarryPotter''
* Synopsis: Welcome to the Avalon Region. Here, children go to Hogwarts, the premiere school for inspiring trainers, where they learn how to train Pokemon. This year promises to be special, for Harry Potter, the destroyer of Voldemort, is coming to take his place among the future trainers and begin his Pokemon Journey.
* Status: The story so far has three sequels: ''[[https://www.fanfiction.net/s/9622964/1/Harry-Potter-and-the-Chamber-of-the-Unown Harry Potter and the Chamber of the Unown]]'', [[https://www.fanfiction.net/s/10190118/1/Harry-Potter-and-the-Lord-of-Sevii Harry Potter and the Lord of Sevii]], ''[[https://www.fanfiction.net/s/10870770/1/Harry-Potter-and-the-Grand-Trainer-Tournament Harry Potter and the Grand Trainer Tournament]]'' as well as a ScrapbookStory, [[https://www.fanfiction.net/s/10123171/1/Tales-of-Avalon Tales of Avalon]].

''[[https://www.fanfiction.net/s/8775086/1/An-Irregular-Trainer An Irregular Trainer]]'' by Sourl3monz
* Recommended by ZeusXenios
* Status: Ongoing
* ''Synopsis'': Crossover fiction between Tower of God and Pokemon. After tasting defeat for the first time, Red feels that he must grow Stronger. By chance he come across a door deep within Mt. Silver. Forcing it open, he enters the Tower. Rated T for violence. It takes place during the first Season of Tower of God and after the events of Pokemon Silver/Gold/Crystal.

''[[https://www.fanfiction.net/s/5954460/1/Total-Pokemon-Island Total Pokemon Island]]'' by ''[[https://www.fanfiction.net/u/1756193/Dark-Amphithere Dark Amphithere]]''
* Recommended by Troopers/PikaScootaloo
* Crossover with ''Literature/TotalDrama''
* Synopsis: Thirty-four Pokemon will travel to an island to compete in challenges for the chance to win one million dollars and a lifetime supply of Poffins. This event is hosted by our lovely hosts, Mew and Mewtwo! Disclaimer: I own nothing except my OCs.
* Status: So far, this series has two completed seasons and one ongoing: ''[[https://www.fanfiction.net/s/5954460/1/Total-Pokemon-Island Total Pokemon Island]]'', ''[[https://www.fanfiction.net/s/6453506/1/Total-Pokemon-World-Tour Total Pokemon World Tour]]'', ''[[https://www.fanfiction.net/s/10536185/1/Total-Pokemon-Redux Total Pokemon Redux!]]''

''[[https://www.fanfiction.net/s/10919574/1/Satori-in-Kalos Satori in Kalos]]'' by [[https://www.fanfiction.net/u/4690685/DeltaNovember DeltaNovember]]
* Recommended by Tropers/{{SpiriTsunami}}
* Crossover with ''VideoGame/TouhouProject''
* Synopsis: Join Komeiji Satori on her journey through the Kalos region as she meets Touhou and Pokemon characters alike, gets in trouble with the notorious Team Flare and uncovers the most legendary of Pokemon. Will she make it all the way to the championship?
* Status: Ongoing
[=[[reviews:Satori in Kalos]]=]

''[[https://forums.spacebattles.com/threads/adorable-murderbeasts-a-young-justice-pokemon-si.358862/ Adorable Murderbeasts]]''
* Recommended by Tropers/{{Mikeal52}}
* Crossover with ''WesternAnimation/YoungJustice''
* ''Synopsis'': One day, Mahmoud Schahed finds himself on the outskirts of Metropolis with a bag, a flute, and six. He knows he's in ''a'' Creator/DCComics universe, but has somehow forgotten ''which'' one, and the important details thereof. One foiled bank robbery and a session with the [[ComicBook/WonderWoman Lasso of Truth]] later, he finds himself taking the name of Trainer Red, and assigned to the Team with Aqualad, Robin, Kid Flash, Superboy, and Miss Martian. As such, this story is about the Self-Insert and his Pokemon, characters in their own right, becoming heroes in the Young Justice universe.
* Status: Ongoing
* Comments:

''[[https://www.fanfiction.net/s/16165/1/Fist-of-the-Pikachu Fist of the Pikachu]]''
* Recommended by Fox Bluereaver
* Crossover with: ''Manga/RanmaOneHalf''
* ''Synopsis'': Due to a technological accident in the Pokémon world, and a botched spell, Ranma Saotome gets pulled out of his own world shortly after separating from his father after receiving his curse. A fateful meeting with a strange electric rodent leads him to explore this new world and live adventures as he never imagined before...
* ''Status'': Dead (last update was in May 2003)
* ''Comments'': It's a shame this story was never continued. Without his father's negative influence, and having Pokémon to take care of, Ranma develops into a much more likeable character, and it's interesting how the author went for developing new customized attacks for Ranma's team, even to the point of getting two of them with a third evolution. Once he gets the female traveling companions, though, they can be somewhat annoying with their constant bickering for attention, but it's still a nice reading. Be mindful that this was written barely when Generation II had just come out, and that it takes a lot from the early seasons of the anime.