The second disc of the game has long been the subject of controversy due to its seemingly unfinished nature, where Fei and Elly narrate the remainder of the game's events as they are shown in a slideshow/montage format with lengthy dialogue scrolls in front of them with little actual gameplay compared to the first disc. For almost two decades since the game's release, there was seemingly no official explanation about the production of the second disc, and fans believed that director Tetsuya Takahashi had more ambitious plans that the development team was forced to ditch because of budget and time constraints imposed by Square.

In a 2017 Kotaku interview with Takahashi, he revealed that while this speculation was correct, there was more to it than that:

"Honestly speaking, what had happened is Xenogears as a project was staffed pretty much entirely out of new staff members, young staff members... Back then, we had the direction of, ‘All projects take two years and that’s when we need to get it done.’ So on top of developing the game, we had to nurture and teach and grow these younger employees. Things like 3D were extremely new, which led to some delays in the schedule. It just wasn’t possible to get everything done."

The higher-ups at Square, when seeing that the team would not be able to reach the deadline in the state they were in, suggested that Takahashi end the game after the first disc when Spoiler:Fei and his team escape from Solaris. However, he did not feel the game's story should have ended there even with the lack of gameplay:

"It was a rough way to end it, and I felt like if we do that, then the players will not be satisfied... so we had a proposal—I proposed that if we do disc 2 in this way that it turned out to be, we can finish the game with the current number of staff and the current time allotted for the schedule and the remaining budget we have."

"I do think my decision was the right one to make, because if we had just ended at Disc 1 it would have been bad."
Contributed by MehDeletingLater
An unused FMV can be found within the data of the game's second disc. The FMV features a song entitled "Stars of Tears", a vocal track performed by Joanne Hogg and composed by Yasunori Mitsuda that doesn't play anywhere else during the game.
Contributed by Gallego13
The Gazel Ministry's personality data is stored in a supercomputer named SOL-9000, a reference to HAL-9000 from Arthur C. Clarke's novel 2001: A Space Odyssey.
Contributed by Gallego13
Food in Solaris is processed in a facility called Soylent System, where Spoiler:they transform Wels (mutant human beings) into food. This is a reference to the movie Soylent Green, in which Spoiler:humans are processed into food.
Contributed by Gallego13
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There is a poster of Tifa from Final Fantasy VII inside a house in Class 2 Citizen Sector in Solaris.
Contributed by Gallego13
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Lucca from the game Chrono Trigger makes a cameo appearance in the village of Lahan.
Contributed by Jrod2004
In the last battle against Solaris' special force The Elements (Dominia, Kelvena, Tolone and Seraphita), they merge their animal-shaped Gears into one big super-Gear in a scene which clearly parodies the Mighty Morphing Power Rangers.
Contributed by Gallego13