WMG / Terranigma

Lord Kumari is the physical incarnation of Gaia.

How else would he know who Ark was and why? The villagers also say that he's the reincarnation of a godlike figure.

Beruga has a Freudian Excuse for his actions.

I mainly thought of this because I found Beruga's characterization rather confusing and somewhat slapdash (why would an apparently logical-thinking scientist turn people into vegetables just so they could live forever, and then decide to kill everyone for no reason?), but I think there is something that could justify everything: After being revered as one of the greatest people on the planet by curing almost all of mankind's ills, he encountered something that he couldn't stop in time: the virus. I can imagine him furiously trying to create a vaccine, and when he's finally finished, walks outside and finds that he's too late. Everyone's already infected (making his vaccine useless, because vaccines don't work if you're already infected, Quintet), so all he can do is watch in horror as everyone he knew died around him before he locked himself in cryostasis. This would take a heavy toll on anyone, and in Beruga's case, causes his mind to snap. He desperately tries to find the secret of immortality, not caring that it turns people into mindless vegetables, because Who cares as long as no one ever has to die again? As for all of his mass murder, it could be because he convinced himself that their lives were meaningless somehow. Perhaps because he feels that they aren't "real" since they're from a different cycle than the one he lived in?

Ark becoming a bird is because of his Dark/Light hero fusion
In Soul Blazer, there are no divisions between Dark or Light hero, because Blazer was created as the original hero. When he was reincarnated as a human, the aspects of his hero-ness were broken up, resulting in the Dark/Light heroes. In Illusion of Gaia, the Dark and Light heroes have to fuse to gain the most powerful ability of Blazer, the Firebird/Pheonix spell. Legends about the Pheonix tie in pretty well with the "reincarnation" theme of the entire series, but take a it a little further.

Ark is the only "hero" that didn't use the Pheonix magic against Dark Gaia; he may not have known he could do it. But in the end, he's forcibly reincarnated as a bird. Probably THE bird; the Pheonix, instead of being used as the ultimate magic against Dark Gaia, is used to give Ark a new form so he can enjoy a reward for all he's done. This isn't entirely out of left field either. In prior games, being killed is almost a slap on the wrist within the context of the game's universe, not merely as a gameplay thing. Dark Gaia told Blazer that he knows Blazer can't die and will just reincarnate and be ready for another fight almost immediately (And that it will happily show Blazer what a curse that is by killing him over and over and over). When Will dies, he wakes up some distance away and experiences a sense of deja-vu but doesn't remember losing the fight (Freedan and Shadow have similar comments if you have the "respawn closer" lives built up). Ark dying and coming back could function similiarly, and the Pheonix magic could have supercharged it enough to let him reincarnate despite being tied to Dark Gaia at the time. The result, a flying Pheonix, representing the power of Dark and Light combined together, flying around the world....

Illusion of Gaia is a DIRECT sequel to Soul Blazer, and Terranigma is a DIRECT sequel to Illusion of Gaia.
At the end of Soul Blazer, the hero vanquishes evil and becomes human. After this, the world tries to separate its dark and light halves so no one gets the idea to summon Deathtoll again, ejecting the Dark Gaia in the form of a malicious comet. The comet however ever is still bound to its origin and passes by corrupting the flow of evolution and effectively putting the world into [1]. Gaia guides heroes of both light and dark to merge to disperse the mass of Dark Gaia that is the comet, they succeed and history corrects itself returning to world to a more industrialized civilization. However, Dark Gaia is STILL part of the planet and once it reforms, it decides to try and rejoin the world through impact.Thus creating the dual worlds cycle in Terranigma, and the hole Ark climbs out of in Chapter 3. Since Light and Dark Arks merge and defeat Dark Gaia in the heart of the world, the cycle breaks destroying Crysta for good but allows Ark to reincarnate as a bird in the world of light. Granted most of the theory relies on things happening that are never said or indicated but I think it fits with the stories of all three games.