Dr. Weil has just been captured, after cursing the Dark Elf and creating Omega, who has wiped out 60% of human population and 90% of Reploid population. All mostly For the Evulz. You'd expect: His captors deem him too dangerous and irredeemable and just kill him already. Instead: They decide to get more "theatrical", thought he could redeem himself, and gave Weil an escapable Fate Worse than Death: seal him in a capsule that prevents aging, but keeps his memory intact, hoping to make him repent. Naturally, when some idiot decades later break the seal down, he becomes more monstrous and vengeful and eventually succeeds in taking over the world and make it so crapsack that it's worse than hell.
The Dark Elf is breaking free and X's body is the only thing he knows that can seal it. You'd expect: He'd tell someone what he's doing and set up a successor or a cover story. Instead: He goes away without so much as a word, resulting in the need to replace him, placing a psychotic Knight Templar clone in charge.
Elpizo is making headway into the Dark Elf's seal with the Baby Elves in tow. You'd expect: Neo Arcadia would dispatch every available resource including and especially the Guardians to intercept Elpizo. Instead: Only Harpuia is sent, while Leviathan and Fafnir dick around waiting to play with Zero.