A fast theory. I am now replaying xenosaga. An important plot element there is labyrinthos.
Labyrinthos in the game is basically on the surface a kind of giant psychiatry. But in secret, there is also a huge underground lab where dangerous experiments are conducted on psychiartry patients and on childlike artificial beings called URTVs. The experiments are intended to establish contact with an extradimensional entity. In the end, the base gets destroyed by a psychic signal called the Song of nephilim which summons alien entities destroying the base.
There is the famous montauk theory by Preston Nichols, claiming the existence of the so called montauk experiments done at the montauk airbase in the USA. While the base had been abandoned, they used a vast underground lab under the base to conduct research. The experiments are claimed to be a continuation of the MKUltra experiments and used children with mental or neurological disorders for experiments. Some experiments served the purpose of communicating with extradimensional entities. In the end, they were forced to admit a psychic signal via the radar dish of the facility which summoned extraterrestrial entities which destroyed the base.
Sounds familiar? I think labyrinthos and the miltian conflict in xenosaga are based on the montauk theory.
But it gets deeper. In xenosaga, the signal in the end causes certain soldiers etc. To be affected by a violent rage. According to Preston Nichols, the montauk signals caused the same effects in wildlife.
Interestingly, the montauk experiments are also said to have summoned people from different times to the base via time travel and in xenosaga 3, at first, it seems the player gets summoned to labyrinthos via time travel.
And there is one last connection. This time not to xenosaga but to the playstation game xenogears which is heavily connected to xenosaga and was developed by the same developers.
According to Preston Nichols, montauk is connected to the Philadelphia experiment and served to save the US Navy ship USS Eldridge.
Xenogears begins with the AI called Deus taking over a spaceship called USS Eldridge.