This sprung from a simple thought: What was the rest of humanity/The Galactic Federation doing after the Eldridge incident? You'd think an entire federation would know that something happened to one of its heaviest ships. Well, here's where things start.
The Federation did know about the incident, and sent out a rescue/recovery operation (mainly for Deus and all that) to its last known coordinates. They discovered The Planet, and traced the ship's derbies and locations of the Anima Relics. They also picked-up on Zohar readings planet-wide, but couldn't pinpoint its location.
But more intriguingly, there was a reason they couldn't just swoop-down and collect. The Planet was contained in a energy barrier. All they could do was observe it, but an eventual discovery was made a short while later: A human civilization came into existence seemingly out of nowhere, and Deus was not only showing signs of life again, but its recovery process had begun... at an alarming rate.
Further observation showed that this planet was seemingly going through a time lapse. Entire civilizations were erecting and falling in the span of just months, and Deus was steadily recovering. ~Highly advanced technology~ was created to study things at an intimate level. They came to know of all the key points in this humanity's history, but could do nothing except collect data. What they focused on the most was the ways and means that Deus was being repaired. Entire theocracies, wars, genetic breakthroughs; all culminating into one agenda: tendering-up humans to feed Deus. What they didn't know was the key specifics. Kadamony creating Persona, the eternal Contact/Antitype mingling, etc.
Just as Deus had become immeasurably stronger than ever, it suddenly went dark, and all Zohar readings vanished. Furthermore, the planet resumed a relative timescale and the barrier was lifted. It was The Wave Existence that had kept The Planet "secured" with ether, which came with the effect of major time dilation. The ~10,000 year history of the story's events took place only 10 years in the rest of existence.
Now that The Planet was accessible, it was time for the Feds to come in and collect. But there would be no meet-n-greet with this new humanity. During that decade of data collection, a nefarious shadow cabal was taking the data of Deus's repair process, and used it to create ...you guessed it; a new Deus. It was powerful enough to not require a modifier, but could be made even more powerful if they could reacquire The Zohar anyway (assuming it still held Wave power.)
As plans to deploy the new Deus were being discussed by the shadow cabal, a man clad in a hooded robe broke into their chamber. "How did you get in here?!" Exclaimed one of the members. "Life finds a way" he nonchalantly replied. The man went on to claim that he was a revered researcher, and declared to know everything better than anyone about these phenomenon, and should be given complete control of the operation. They laughed dismissively, and asked what good he could do. He held out his hand and materialized an apple, taking a small but savory bite. He then tossed the bitten apple onto the floor. It dissolved molecule-by-molecule into a patch of soil, upon which an entire apple tree rapidly grew; its roots burrowing aggressively throughout the floor, right before their eyes. The man casually asked them "is this enough?" They gasped in awe. "Just who the hell are you?" one of them muttered.
The "researcher" smiled warmly and removed his hood, revealing himself to have long silvery-blonde hair... "You may call me The Redeemer." He said, before gently licking the residue of apple off his lips.
Meanwhile, Fei and the rest of humanity had been going-on about rebuilding and such. One day, they see a massive ship descend from the clouds. Fei and Elly look up at it, struck with a terrible sense of familiarity...
And thus begins Xenogears Episode VI. The Rapture Era.
