[Edited again to add integral Blue Star Memory key details]
Yep. You have it right Thoul.
~Ragolians or something traps the Great Shadow in the Photon Flow of Ragol.
-People lived on Ragol (Ragolians)
-Ragolians find d-cells/Germ and Dark Falz is born
~Great War, Leukon Knights used, Dark Falz defeated
~Dark Falz unable to be defeated because of photon weaponry and sealed
-Ragolians evacuate and move to Coral - Almost all Ragolians wiped out
-Dark Falz stirs 1000 years later and sends meteor
~Dr Montague finds d-cells, makes mags, Mother project, Pioneer 1 departs for Ragol
~Pioneer 2 shows up under false pretense of "dying planet"
-PSO 1, 2, and 4 happen
~A second smaller explosions happens after Episode 2 and people's mags begin to non function. Everything relying on D-cells on Pioneer 2 ceases to function. Chaos ensues.~
~Episode IV begins with a meteor with d-cells launched towards Coral but is hit by a laser beam from Ragol and hits Pioneer 2 before landing on Ragol. This leads to the meteor being investigated.
~Mother Trinity is installed on Coral. (Mother Trinity is Mother Brain with 3 AIs)
~Mother Trinity begins to be slowly corrupted by the influence of D-cells (Dark Falz origin)
~Blue Star Memories happen
~Sometime during episode 1/2/4, Tyrell is ousted by Dol Grisen and Grisen declares independance from Coral. A short war is fought
~OPSS incident, Pioneer 2 gains independance from Coral
~Episode 3 happens
~Pioneer 2 finally lands on Ragol and colonizes it and everyone lives happily ever after
The Following is taken from the dialogue of Phantasy Star Zero and put in order:
~On Coral, Newmans are improved and perfected with the work of Mother Trinity
~Mother Trinity takes care of Coral and the people of Coral continue to polute and fight and ignore her
~Mother Trinity gets angry and starts wiping out humanity on Coral
~Mother Trinity moves to Arca (Moon) and bombs mankind back to the stoneage
~Mankind on Coral goes into a period called "The Great Blank" and much knowledge is forgotten
~Mother Trinity ressurects the Newmans as her slaves and servants since they are superior to humans
~During the Great Blank, people forget the name of the planet and the moon
~A word referring to dirt gradually becomes a reference to the planet, itself - Earth. No one cares about giving the moon a name.
~Humans re-emerge on the surface of the planet, and begin rebuilding.
~Humans find Casts, and begin re-activating them. The Humans and casts then begin a fledgeling civilization.
~Phantasy Star Zero occurs.
According to Episode 1, 2 and 3, Dark Falz is born from d-cells finding the perfect host and merging completely. AKA Rico, Aka Flowen (almost)
if you want, I'll cut and paste the dialogue that correlates most of this.
I am trying to put it in a DOC file with the script used and you can read it and come to a conclusion.
Hey Thoul? This is for you. I've searched the EPISODE 3 script and pulled everything out pertaining to this topic. Next I'll quote the stuff from Episode 1/2 that backs up the Coralians originating on Ragol.
Most of this document backs up that timeline up there. It also gives insight as to WHY Dark Falz could never be defeated. Why Pioneer 1 exploded and why Photon Weaponry CANNOT kill it.
When you read it, you'll also see that BLITZ suffered the same fate Flowen did. Flowen became infected by GERM/D-CELLS like Blitz did. Blitz was the second attempt to merge.
For a grander note, Blitz is Bernie. Kylria's mother is Alicia Baz. Kylria and Kranz are brother and sister.
Episode 3 info
http://www.megaupload.com/?d=F0VBOBV4Episode 1,2,4 info
http://www.megaupload.com/?d=W0XT6VMEBesides, I love the design of Leukon Knights

P.S. I found the information from episode 1/2 and uploaded it and then I've also added what you learn from PS Zero. The episode 3 info explains the nature of Dark Falz/Great Shadow. You can relate the Great Shadow = Profound Darkness and Dark Falz = Dark Force.
The Great Shadow in itself is not evil. it just produces the GERM because that is all it can do. GERM has a mind of its own and seeks out the best candidate to mutate and evolve. I think Dark Falz, which grows from the Germ, wishes to escape from Ragol where it is trapped.