The second disc of the game has long been the subject of controversy due to its seemingly unfinished nature, where Fei and Elly sit in an empty area and 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 and 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:


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:

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.

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.

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.

There is a poster of Tifa from Final Fantasy VII inside a house in Class 2 Citizen Sector in Solaris.

Lucca from the game Chrono Trigger makes a cameo appearance in the village of Lahan.

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.