Puzzles
The main challenges the player will face in Atlantis will be in the form of puzzles. These puzzles include learning how to use Atlantian technology and decoding the Atlantian language. As the player solves these puzzles, more of the story will be revealed and the player will gain access to new areas. The player's goal is to reach the Shrine, and then the chamber of the devote leader.
Some potential ideas for possible puzzles and devices are listed below:
Atlantian Power
The Atlantians were able to utilize power from the extreme energy within the Earth's mantle. They created a large device and placed it underneath the ocean that would drill down to the mantle, and extract the energy inside the mantle. The energy would then flow through pipes from the ocean's floor and up into a power facility that would disperse the energy around the island. A enclosed structure was created that would allow Atlantian workers to travel down to the ocean floor to calibrate the drilling device.
When the player arrives, there is no power to any part of the island. When the player gets in the power facility, he finds out that the drilling device used to extract energy has been calibrated incorrectly. (One of the workers probably calibrated it incorrectly on purpose during the war to cut off power) The player has to travel down to the ocean floor through the enclosed structure and recalibrate the drilling device. The device will then start up again, and power will be restored to the island, allowing the player to further explore the island. About.com Mantle article
The Rain Machine
An observatory sits high up on one of the mountains of Atlantis. The observatory consists of the home as well as the laboratory of a scientist. This particular scientist had a little issue with the weather - on the scientist's wedding day, lightning struck the scientist's husband, and her husband died. From that time on the scientist researched and performed tests on ways to control the weather. The scientist hoped to rid the Earth of lightning storms all together. Although the scientist was never successful in controlling lightning, the scientist was able to create a machine that would increase the amount of precipitation in the clouds, and cause rain to fall from the clouds. Indeed, the scientist had discovered quite an advanced form of cloud seeding.
One thought I had for the rain machine is that it could be used by the player to fill up a canyon. Perhaps there is a very steep mountain in the middle of a canyon that the player can't get to. In order to reach the top of the steep mountain, the player could use the rain machine to fill the canyon with water, and then swim over to reach the top of the steep mountain. Of course, the player would have to tell the rain machine where to seed the clouds so that only the cloud over the canyon would burst forth with rain. And, of course, this would take much, much, much rain.