Yami Yugi, known as Dark Yugi in the manga and Japanese versions, and also referred to as the Nameless Pharaoh, is the spirit of Pharaoh Atem that has been sealed in the Millennium Puzzle. He is the main protagonist of the original and second series, along with Yugi Muto.
Together with Yugi he holds the title "King of Games" (King of Duelists in Japanese version), by winning in the Duelist Kingdom, Battle City, Grand Championship and Battle City V2 (in GX anime) tournaments.
After Yugi Muto solved the Millennium Puzzle, Yami Yugi resided in Yugi's body and would take possession of it when Yugi or his friends were in danger. After Yugi became fully aware of Yami's existence, Yugi could voluntarily give control of his body to the Pharaoh; occasionally before one would give control to the other, they would, as souls in the mind of the one controlling Yugi's body, converse with each other, usually about their options of what to do when in difficult situations.
Ikran's F-Zero timeline[]

Yami (middle), with Joey, Tinsel and Yugi in Port Town, representing Falcon's sidekicks

Yami as he shattered the Skull's bones
Yami, as Yugi, along with Joey, Tea, and Tristan were saved by Tinsel and her Silver Comet just as the island of the Battle City tournament was about to explode by Kaiba! Since then, he became curious of the sport, F-Zero! And Tinsel took him and Joey on an adventure starting at Port Town! When they arrived, they came across a punk Duelist who challenged them; Dueling was rare outside of Earth in favor of the racing tournament. He and Joey won seamlessly, though he missed the Blue Falcon that Tinsel saw! Yugi became fascinated with the elitist, much like him, and so they embarked on a personal journey following him!
From Red Canyon, to watching the Casino Palace Bet race, to overcoming the Bloody Chain with Multiplying Kuriboh, to saving Falcon from an exploding power plant in Lighting with Slifer, Yugi transformed into Yami and he escorted Falcon and Jody out of the exploding powerplant! He then encountering the intimidating Black Shadow!! Yugi and Joey figured he'd be from the Shadow Realm, both as Duelist and racer, though Tinsel and Joey chased after the hapless Blue Falcon attached with a speed-sensitive bomb! Joey got all washed up and returned to Mute City before they should get struck! The GX Grand Prix was coming up, and Falcon reunited with Tinsel! He thanked him and Joey for saving his hides in a unique way. They prepared their Monsters and watched over the race, then Falcon and Tinsel were successful, till Deathborn complicated things. Yami sensed the evil presence before his emergence killing off Black Shadow! By the next day, Yugi was reluctant on helping Falcon, though Yami convinced him otherwise. He didn't emerge after that, but Falcon freed him and his friends, and they shall look forward to visiting him again, as long as they keep their word on keeping the fortress' location a secret.
Over a year later, Yugi got the call from Tinsel, saying that Dark Million has raised the bar and wreaked havoc. He and Joey were involved in the incident during the Fake Star race, transforming into Yami and riding Curse of Dragon! He unloaded Kuriboh and blew up the blimp, while attacking it from outside! Then, he received a message Tinsel has quit dueling just after he encountered Dartz and how he was nearly controlled by the Seal of Orachalos. By the time the Dragons were awakened, and the Great Leviathan was frozen, then shattered, Domino City was unfrozen, and he soon reunited with Tinsel looking for the Task Force! He and Joey met Rick and schemed their plans at the King League course. He and Joey hung out at the Port Town Queen League circuit for a short while, before they assisted Jody against a swarm of Dark Soldiers. However...it was only a ploy as they were captured by her within the minefield!
Leon was able to find and rescue them, only to behold the sight of his old nemesis, Black Shadow!! He headed to Dark Star to save Tinsel and the universe, and hung out in the Falcon Flyer. Yami emerged as they teams approached Dark Star and he used several of his Duel Monsters including the Five-Star Twilight, Curse of Dragon, and even the Magnetic Trio! He soon beheld Planet Uma-51 being imploded by Dark Star's fatal orbitting sensors, and assured everyone they must remain calm and as a team to beat the odds. Yami was able to shatter the Skull's bones and endure Black Shadow's umbrakinesis...till his shell shattered and emerged as Deathborn!! His darkness was too much for the Millennium Puzzle rendering the pharaoh powerless. He reverted back to Yugi, and he listened in on the legend from Falcon; that Rick's the savior of the galaxy, as the Wuji/Dragon, the neutral element that can help turn the war in his favor! By the time Deathborn, Dark Star, and Falcon were incinerated by Rick's Full Power Booster Fire, Yugi mourned for his loss. Yami, as a holy spirit, emerged again as the Eye of Wjat was restored, thanking everyone for saving the universe, and he considers them all to be his Champions.
A little afterwards, he was able to get his memories back, and challenged Yugi to a final duel, and he won over him and wished him farewell.. A few years later, he was invited to Tinsel and Rick's wedding on Oct. 9, 2577, and Yami, err Atem, can't attend... The last duel was against Diva, and Yugi disassembled the Puzzle afterwards allowing the spirit to rest! He currently resides in the heavens with the elitist, Capt. Falcon; the engineer, Dr. Theodore Clash; Haruka's kindred spirit; and Kaiba. It's rumored he was the one who conjured a meteor shower and destroyed the Desert Kingdom after Rick left as he almost got charmed by Princia.