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There's a fanfic called "Atlantis: Heritage" on Fanfiction.net
Here's what the summary says.
The story takes place after the planet expedition. Jim's father seems to have an obsession with the legendary Atlantis, and the whole family bloodline was connected to it. Will the two discover the truth of many Mystery? Death of Milo's parent? Who is Pleiades Hawkins? And what part do they serve in the legend of Atlantis? The Adventure begins, 1914 "The Benbow Inn" Montressor.
After reading this, I couldn't help but think of an AU where Jim Hawkins is an Atlantis descendant.
I love this story so much that I can't help but think of what would happen in the Crystal Chamber. (It hasn't been updated since 2018.)
As the stones deescalated to the secret chamber, Jim, Milo, Kida, Rourke, Helga, Dr. Doppler, and Captain Amilia gaze up in awe at a giant blue ball that looks so much like a sun, surrounded by ten huge carved stone faces.
This is the Heart of Atlantis.
"Upon my word." said Delbert.
"Jackpot!" said Rourke.
Everyone stared up in awe at the crystal, Kida let out a gasp as she bowed down and gave the kings of her people's past prayers.
"Thatch, tell her to wrap it up, we got a schedule to keep." Rourke ordered.
Milo did just that, reluctantly.
Rourke then kicks a small rock into the water and the crystal shines red lights, making the group of seven worried about what's going to happen next.
Helga announces, "Come on, let's get this over with. I don't like this place"
Rourke turns to Milo and demands answers from him, "All right, Thatch, what's next?"
"OK, there's a giant crystal hovering 150 feet above our heads over a bottomless pit of water. Doesn't anything surprise you?"
Milo goes off at Rourke about what is happening right now and just grasping at straws. The red light shines over onto Jim, turning back to its crystal blue color.
His earring starts to glow again
"Pahtim?"
"Jim?"
Delbert asked the cabin boy if he was okay, but got no response from him. Jim's eyes began to glow exactly like the crystal's and his hair turned white again.
Delbert, Amilia, and Helga try to call out to Jim, but Jim walks to the edge of the water before stopping at the brink of the shore.
Milo and Rourke's argument stops when they notice Jim's trances.
"Talk to me, Thatch. What's happening?"
Milo "Look, all it says here is that the crystal is alive somehow. It... I don't know how to explain it. It's their deity. It's their power source."
Rourke "Speak English, professor."
Milo "They're part of it. It's a part of them. L... I'm doing the best I can here."
Rourke reaches for his gun, "Well, do better."
Fed up with Rourke's threats and demands, Milo retaliated, "Oh, I know. Why don't you translate, and I'll wave the gun around!"
Jim turned to the group and spoke in fluent Atlantian. Telling Delbert, Amilia, Helga, Milo, and Kida that everything will be well, and to not be afraid.
Rourke looks at Milo and asks, "What did he say?"
"I don't know, I didn't catch it." Milo admits.
However, Kida said in a quiet voice to everyone, but Rourke. "The crystal is calling Jim to it... Just like my mother."
Jim turns his gaze back to the crystal and starts walking again. However, instead of walking into the water, he walks on the surface of the water. Causing everyone's eyes to wide in shock and amaze.
As Jim made his way under the floating crystal, the giant slabs of the kings expanded as the other rays of light gathered towards the center. A strong energy blasts from Jim's crystal as his loses consciousness.
Then without any delay, the crystal lifted him to itself as the stones circled him, spins faster and faster.
Soon, the crystal morphs and changes into a human shape. A familiar human shape.
The crystal has been infused with Jim.
Jim Hawkins has bonded with the crystal.
The now crystal-fused Jim descends from the sky and gracefully lands on the water's surface again.
Before Delbert or Amilia could run to Jim, Rourke held them back. "Hold on there, Doc and Captain."
Amilia "Jim."
Jim opens his eyes, instead of his normal blue eyes, they are glowing light blue. Like the crystal.
Delbert and Milo, "Jim..."
Kida, "No..."
Jim walks back to the group, as the giant boulders of the past kings fall to the waters, splashing around him. However, not a single drop got onto Jim, for the crystal's energy is strong enough to make a force field.
As Jim makes his way back to dryland, Rourke tries to grab his arm, but Milo stops him from touching him.
Meanwhile, Helga was at a loss for words. She wanted to get rich but at the cost of Jim's life.
The only thought that ran in Helga's mind was, 'Why must history repeat itself?'
This is just an idea of what I imagine of what the future chapter could be.
But I can imagine this story becoming an AU crossover.