Pocket Monsters BW: Good Partners is a Pokémon manga based on the games Pokémon Black and White.

A manga adaption of the original video game.

Link, a shepherd from Ordon Village, sees village children, including with his childhood friend Ilia, being kidnapped by monsters. He chases after them only to find his world covered in twilight. Thereupon Link suddenly transforms into a wolf and finds a mysterious character named Midna. His journey to bring back light into the world begins.

"Ness' Great Adventure, a manga comic that closely follows the story of Mother 2, in the comic, like Mother 2 it includes weird humor and interesting uses for items much like the "Help!" description option in Mother 2. Added in this comic are discussions between Itoi, Itoh (the guy who drew this manga, and also did the character design in Mother 2) and Kohichi Ohyama (Art Director), who talk about what the actual meaning of "Mother" is, and other stuff." - from Starmen.net

A 2 volume manga that explores the origins of Samus Aran.

An E-Manga was made for chapters 1 and 2.
(http://www.mechadrake.com/metroidmanga.html )

In yet another area of the Pokémon world, there are no trainers, only rangers who temporarily borrow the service of wild Pokémon for good.

The main character finds himself on an almost impossible mission and hopefully, with the powers he has borrowed from the Pokémon he has gathered, he will discover a way to stop the evildoers who have started havoc.

Hitomi is a Pokemon Ranger; someone who uses wild Pokémon to achieve their goals rather than capturing them. While Pokémon Rangers don't need Poké Balls to capture Pokémon, they do use a tool called a Capture Styler in order to form a bond of friendship with the wild Pokémon. Two years after Hitomi's graduation from the Ranger School, she joins a team with a Top Ranger. This Ranger uses a rare type of styler called a Vatonage Styler, which is only available to Top Rangers. Just what kind of skills does this Top Ranger have, and more importantly, how exactly does the Vatonage Styler work?

The protagonists are Ryouga, a boy with superhuman strength, and Miruto, a girl who works for an organization tracking the villains. The plot centers around "Burst", the ability to use crystals with Pokémon stored in them to transform into human-Pokémon hybrids. Ryouga's Burst is Zekrom, and one of the villains' is Excadrill.
On rare occasions they actually use Pokémon.

Back Story:

Taking place on the fictional continent of Elibe and staring Roy, the son of Fire Emblem protagonist Eliwood. Roy leads the League of Lycia's army against the forces of the militant country of Bern shortly after his father falls ill.

The story begins when King Zephiel, ruler of the kingdom of Bern, finishes the brutal conquest of Ilia and Sacae and sets his sights on Lycia. With the war coming to his own country, Roy is sent home to lead Pherae's army to oppose Bern, but soon after he meets Guinevere, the princess of Bern and Zephiel's younger sister, who has escaped from her homeland to search for a way to stop the imminent war between Bern and Lycia.

Upon the death of marquess Hector, Roy carries on the Lycian League and makes many promises: to protect Princess Guinevere and Hector's beloved daughter, the mage Lilina, and most importantly, to save the entire continent from Zephiel's mysterious thirst for world domination.

Featured Story:
But this story's hero is Al, son of a Bernian blacksmith. After turning 15, he left his home with his father's sword to go on an adventure in this continent bound for war.


Side Story of Fire Emblem: Binding Blade (Gameboy Advance Videogame).

From Viz:

Pokémon comics based on the original Game Boy games... not the TV series!

POKÉMON ADVENTURES includes all the Gym Leaders, places, and opponents from the game. There's plenty of action as trainers named Red and Blue explore forests, jungles, cities, and caves in search of Pokémon and excitement. But can they foil the schemes of Team Rocket, a mysterious group of villains who want to use Pokémon for evil?

Vol 1-7: Red, Green, Blue & Yellow
Vol 8-14: Gold & Silver
Vol 15-22: Ruby & Sapphire
Vol 23-25: FireRed & LeafGreen
Vol 26-29: Emerald
Vol 30-40: Diamond, Pearl & Platinum
Vol 41-42: HeartGold & SoulSilver
Vol 43-51: Black & White
Vol 52-ongoing: Black 2 & White 2