Basically, everything is cannon(ish) until the end of the dialogue (which I'm taking from the subbed version).

Tears filled Yuugi's eyes as the Silent Magician completed her attack and rid Atem of the former Pharaoh's remaining life points. Falling to his knees, Yuugi's entire being rebelled against the idea of losing his best friend, his confidante…

And the person he loved most.

Yuugi barely registered Atem as he crouched before Yuugi, and startled at the comforting hand that landed on his shoulder.

"Stand up," the Pharaoh commanded, "The winner shouldn't be on his knees. If I were you, I wouldn't cry."

Yuugi tried to swallow his sobs. "I-I'm too weak…You've always been my goal! I always wanted to be strong…like you."

A gentle smile crossed Atem's face as his fingers tightened on Yuugi's shoulder. "You're not weak. You've always had a power that no one else could beat…The strength of kindness! That's what I learned from you.

"Aibou…" Atem put both hands on Yuugi's shoulders, encouraging the shorter boy to stand with him, "The courage you showed me when you accepted this Battle Ceremony showed me the path that I must take."

"Other me…" Yuugi muttered.

"I'm not the 'other you' anymore," Atem replied. "And you are no one but yourself! You're the only Mutou Yuugi in the world!"

Though tears were still in the corners of his eyes, Yuugi valiantly put on a brave face and nodded. Suddenly, the eye of Wadjet lit up brilliantly, and Yuugi knew it was time to say goodbye.

"You're not the 'other me' anymore…" Yuugi whispered to himself. As Atem faced the doorway, Yuugi suddenly reached forward, grasping desperately at the Pharaoh's wrist.

"If you're not the 'other me' anymore…you're Atem! And you're the only Atem in the world!"

Atem smiled kindly, his hand coming to rest upon Yuugi's with an encouraging squeeze.

"And that means you're your own person and that I can say that…that I love you," Yuugi's hand tightened, silently begging for the Pharaoh to understand. Atem's eyes widened in shock, before a happy expression settled on his face.

"Yuugi…" Atem drew the shorter boy close, hugging him tightly. "Can I assume this means you want me to stay?"

Yuugi nodded frantically. "Please don't go."

Isis' eyes were sad as she replied for the Pharaoh. "The spirits of the dead are not meant to linger among the living. The Pharaoh must pass on, Yuugi."

"There are loopholes, though," Atem said, shrewdly. "If I were to pass on and then come back, technically, I'd have been to the afterlife as I was supposed to and then I would come back with a blank slate."

Isis' eyebrow twitched. "I…I suppose that is true, Pharaoh, but there is no time to discuss that now and I do not believe we could find such a way."

"I dunno," Jou grinned. "I could go for another adventure that includes life or death situations. Otherwise, I'd be bored outta my mind."

Seto rolled his eyes. "Great. Just when I thought I'd be rid of you people…"

The entire cavern rumbled and small pebbles fell from the ceiling. Marik looked around, panicky, as he felt the universe become restless with their stalling. "Guys, we're messing with things we don't have any chance of understanding. We'll all miss you, Pharaoh, but could you kindly die already?"

"Man, I live half my life without fully understanding anything," Jou snorted, "I say we stall as long as we need to."

Yuugi pulled away from Atem and looked up into crimson eyes. "Atem…do you want to stay? With me?"

"Is that okay with Jii-chan?" Atem joked.

Said grandfather rolled his eyes. "Like I have a choice. You know how Yuugi gets when he wants something."

A mischievous light entered Atem's eyes. "Yes…Yes, I do know how Yuugi gets."

The cavern gave another great rumble, the occupants having to throw themselves to the side to avoid being crushed by falling debris.

"Not that this isn't super sweet and all," Mokuba complained, covering his head, "But can we please decide on what we're doing and get the hell out?!"

"Atem!" Yuugi cried, desperately.

The kindess returned to the Pharaoh's countenance, and his hands settled on Yuugi's cheeks. "Yuugi…I have to go. Our purpose as two souls in one body is done; the millennium items will only be sealed if my soul goes to the afterlife. I have to go through that doorway."

Tears rolled down Yuugi's face as he buried himself in Atem's chest.

"You're strong enough now, Yuugi," Atem whispered, hugging the other close, "You've always been strong enough. You don't need to follow me anymore. You should…no, you will follow your own path."

As Yuugi sobbed, he paid no attention to the falling rocks, the screams of his friends…

Or the stealthy hand that slipped into his deck holster.

"But, we will meet again, Yuugi," Atem said with conviction, causing Yuugi to pull away and stare up at Atem.

"We…we will?" he asked hopefully.

"We'd better," Atem smirked, that mischievous expression back on his face in full force, "Or you'll never get your deck back."

Yuugi pulled away completely, surprised. "What're you…?"

A wicked grin pulled across Atem's face as he waved the aforementioned cards in his hand.

"How did you—!" Yuugi cried, looking into his holster for his cards—true to Atem's word, the Pharaoh had somehow snuck out his entire deck, side deck included.

Atem jogged towards the light in the doorway, a smile on his face. "Yuugi! If you want your cards back—if you want me back—figure out a way! I'll be waiting for you!"

The leather pants and jacket turned in a mauve cape and a white tunic and the son of Aknamkanon returned to proper death, leaving a gaping Mutou Yuugi behind. The door shut before the young duelist could react; before his wits were gathered, the group dragged him away as the cavern collapsed entirely.

The millennium items were sealed forever; Isis and Marik were free to live their lives and no longer had to serve the Pharaoh; the adventure was over and the world was safe.

"I'd call that a win," Otogi shrugged.

"He took my freaking deck!" Yuugi raged, stomping around and kicking up sand, "And he expects me to figure out a way to bring him back to life so he can return the cards he stole!"

Anzu smiled uncertainly, "Well…even when he's gone, other Yuugi sure knows how to keep things lively."

"Atem," Jou corrected. "And we'd better figure out how to get him back soon, before Yuugi has a coronary."

Honda sighed. "Just when I thought we'd be normal high schoolers again…"

Jou looked at Seto expectantly. Annoyed, the brunet huffed.

"What, Jou?"

"I hope you don't think you're staying out of this, Kaiba."

"Are we expected to help, too?" Marik asked, somewhat resigned.

"Of course!" Anzu replied. "We're all helping! There's no way Yuugi's giving up, and we shouldn't either. Atem gave up his soul so that the world would be safe—he's lived nothing but an unselfish life. All he wants to is to be cute with Yuugi and we're gonna make sure it happens!"

"If Yuugi doesn't kill him first." Rishid said, deadpan.

"Yuugi doesn't have the heart," Sugoroku laughed confidently.

"Atem! Come back to life this instant and give me back my deck, you narcissistic, parasitic, selfish asshole! GIVE ME BACK MY DECK!" Yuugi screeched to the ground, stomping on it for good measure.

Atem walked toward his former council and friends, smiling at them as he approached. On his chest, he felt the familiar and comforting weight of the millennium puzzle.

"It has been too long, my friend," Mahado declared as he stepped forward, hugging the Pharaoh.

"It has," Atem agreed, and similarly greeted the others. "But I'm afraid I won't be here long."

Mana frowned. "But…your destiny is completed, Atem. You don't have any reason to remain amongst the living. Your story is over."

Atem grinned, his hands encircling the puzzle and giving the others a glimpse of an absolutely pissed off Mutou Yuugi.

"…you narcissistic, parasitic, selfish asshole! GIVE ME BACK MY DECK!"

"My friends, my story has only just begun."

I hate myself. Someone stop me.