A:
Mage King Solomon’s repudiation of mankind.
The old HCSO researchers sending Laplaces to the BC era caused Solomon to find out about the future, and be enraged at the facts that magecraft died out and humanity became the prime species.
After steeling his heart with feelings about the inevitability of their demise, he broke the Holy Grail into pieces and derailed history, all in attempt to change the future.
The launch of LAPLACE made it impossible for Solomon to alter the results of history up to 2015, thus, he resorted to turning the Holy Grail into singularities to derail history. Something to that effect.
B:
Solomon’s salvation of mankind.
The big twist is that only Solomon knew the truth about the discontinuation of history post-2016.
The culprit is the Earth Model created by the HCSO.
The Earth Model is a “God Egg” made by compiling data from Earth. Humanity’s malice is among the things cultivated inside it, and the unfortunate consequence of that is that the egg would eventually hatch into an “Evil of Humanity.”
Solomon attempted to derail history and exterminate the HCSO in order to destroy the Earth Model.
If this option is chosen, the boss battle will be against the Beast born from the Earth Model.
…Using the Earth Model as the final boss would spell the end of the game’s core narrative mechanics, so consider this one the Hail Mary option to end the game’s service.