The Xenogears game has a rather curious endgame message: ``Xenogears Episode V, The End''. I came across the following bit of information regarding why this is the ``fifth'' episode of the story. This page has since been extended based on the contents of the Xenogears: Perfect Works book released by Square.
Episode I: Happens in 2510AD, approximately 15000 years before Xenogears
The era began with the discovery of the Wave Existence's universe. A new time period began, denoted TC for ``Transcends Christ''. It was during this time that humans designed the trap for Zohar (the Wave Existence).
During the next era, research on Deus began; in the period up until 4768 T.C., the Zohar Modifier was constructed on a universal transport and sent to the end of the universe to test its power. When this transport returned to Earth, they discovered it was unreachable, protected by a mysterious force. Humans aboard were forced to find a new planet to settle on -- their ``New Jerusalem''. Toward the end of this journey, Project Deus is constructed aboard the Eldridge.
Episode II: Abel makes Contact with Zohar on the Eldridge, 10000 years ago.
In 4768 T.C., before the project was completed, Deus took over the Zohar and the Eldridge, and attempted to return to Earth. The captain ordered evacuation, but Deus took over weapons systems and destroyed almost all of the escape craft. In the end, the captain activated the self destruct system. The wreckage of the Eldridge crashed on a nearby planet.
One human, Abel, survived -- or rather was saved by Zohar. Zohar created Elhaym, and at the same time Deus activated ``System Hawwa'', creating Miang. Throughout the course of history, Elhaym took the traits of Mother and retained Zohar's purpose, while Miang took the traits of Guardian and retained Deus's purpose. The Urobolus Factor originates in Elhaym and Miang, guaranteeing their traits would be carried throughout time until they eventually merge (Urobolus == ``infinity'').
The crash of the Eldridge on the planet marks the beginning of a new calendar system, simply Year 0. It was also at this time that Cain and the Gazel Ministry came into existence.
Episode III: Fall of the Zeboim culture, 4000 years ago.
The Zeboim are the civilization hinted to at the bottom of the Lighthouse during Xenogears. Their technology was very similar to modern (real) Earth. Through Miang's influence on the Prime Minister of Aquavy, a war was initiated between Aquavy and Ignas. The resulting nuclear war rendered most of the world uninhabitable and humanity was almost destroyed. The Zeboim culture fell in Year 6086.
It is also during this period that Emeralda was created by the era's versions of Fei and Elly. These events are alluded to during the exploration of the underwater reactor where Emeralda is first discovered.
The history is quiet for the next 3000 years, but around Year 9100, construction of Etrenak, the city of the Solarans, begins. Within the next century, construction of Shevat begins atop Babel Tower.
Episode IV: Diablos war between Solaris, Shevat... 500 years ago.
In Year 9500, Sophia established the religion in Nisan, becoming the Mother of Nisan. As she gained a following, Solaris began to view her gathering as an uprising of the lambs. Solaris attacked Nisan, and early on Shevat joined with Nisan in the war. Five years later, Queen Zephyr was approached by Cain, and eventually agreed with Solaris to trade Sophia for Miang, the instigator of the war. Sophia sacrificed herself to attempt to reverse the treachery of Zephyr, however in the end Nisan was devastated.
Shortly after the death of Sophia, Lacan made contact with the Zohar modifier and was transformed into Grahf. Grahf destroyed almost all civilization during what was known as the Diablos war; Grahf also destroyed the bodies of the ministry. Their deaths released the Anima Relics; the Omnigears were created, and Roni Fatima and Zephyr were able to stop Grahf. Grahf disappeared, and Krelian entered the story by storing the memories and personalities of the Gazel Ministry within the SOL9000.
Episode V: Xenogears, present time.
In the next several centuries, Krelian worked toward the resurrection, going as far as creating the artificial Contact in 9975. During this time, Fei was also born, and Miang possessed his mother. Miang forced Fei to undergo testing, where it was revealed that Fei was the real Contact.
Several years later, Grahf appeared to try to take Fei, and fought Fei's father. The conflict, as well as the stress Fei went through during the testing, finally allowed ``Id'' to surface. Around this time, the game of Xenogears picks up; the recent history leading up to the game, as well as the events of the game itself, are fairly apparent. In the end, Elly and Miang merge, the Contact/Anti-Type cycle is broken, and Urobolus is destroyed.
Episode VI: Occurs shortly after Xenogears.
Very little is currently known about what Episode VI encompasses.
Xenogears is Episode V, and there is a new game in the works called Xenosaga which will cover Episode I. At this time, not much is known about the new game, except that it is being produced by many of the same people who produced Xenogears, but by a different company -- Monolith Soft.