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The SOL-9000 is a large spherical computer that contains the digital versions of eight members of the Gazel Ministry. They are seen as blue and red faces in the "fishbowl-like" ship, called the Ezekiel, throughout the game.
After the physical deaths of the Gazel Ministry members 500 years prior to Xenogears Episode V, this machine was constructed in 9506 by Karellen, at the request of Cain, to hold their data and personalities. The SOL-9000 was the only machine that could activate the Gaetia Key.
When the Gazel Ministry activated the Gaetia Key, they were no longer of any use to Karellen, who slowly erased the Gazel Ministry from the SOL-9000. This also gave Karellen complete control over Project Noah and a chance to begin the Ark Plan.
Etymology
"Sol" is the Latin word for "sun", and is also the name of at least one deity in Ancient Rome, who was the personification or associated with the sun.
The numerical value may have been a reference HAL 9000, the infamous main computer of the USSC Discovery from Arthur C. Clarke's 2001: A Space Odyssey. The scene where Karellen erased the Ministry is also reminiscent of the scene where Dave unplugs HAL. The 9000 could also be a reference to it being built and used in the E.C. 9000s in the Xenogears timeline.
Another possibility is the "SOL 9000" satellite weapon (SOL possibly standing for Satellite Orbital Laser, a reference to the sun, or possibly both) from the movie Akira.