Mt. Aleph is the supposed "beginning of all" in the world of Golden Sun and the home of all psynergy. It houses the 4 elemental stars. It is also the home of the almighty being, the Wise One who is a being who has ultimate power and can use all forms of psynergy. Mt. Aleph boarders Vale, meaning that Vale gets the direct psynergy flow as it comes down the mountain. Mt. Aleph is also the producer of all those Psynergy Stones you see lying around after the explosion that took place when Isaac and Garet escaped when Saturos and Menardi to the elemental stars.
 Story Information
Throughout Mt. Aleph there are traps and puzzles to protect the stars from greedy thieves and people seeking power from the elemental stars. During the younger years of Isaac and company's lives, Saturos and Mendari triggered one of these traps when they tried to scale Mt. Aleph to take the power they sought to save Prox. During this time, Isaac met with Saturos and Menardi and was felled to them. After a few years, Isaac and company scaled Mt. Aleph for studying purposes, and passed the traps and puzzles the were presented to them and got to the elemental stars. However, due to Saturos and Mendari, Issac and Garet were forced into giving the elemental stars to them, in which started a chain reaction which caused the entire mountain to explode. However, thanks to the Wise One, both Isaac and Garet escaped and were charged with returning the elemental stars to their places on the mountain. After Isaac and Garet leave Vale, they can never return to Mt. Aleph.
However, they are able to view Mt. Aleph once again. Once the party beats the game on Golden Sun: The Lost Age, you will return to the sight of Mt. Aleph sinking into the ground. Though, after this event (being the end of the game) it really gives you no information on whether or not Mt. Aleph will play an important role in the next game. You are also able to view the mountain on the cut scene with Alex and the Wise One.
 Fun Fact
Did you know that with the glitch on Golden Sun: The Lost Age that you can return on the land where Vale and Mt. Aleph lay and actually go see them? However you cannot enter the towns that you can see.