The final boss is Kino.
When the Gigasaurs cornered him on the hill, Kino realized his latent powers that stemmed from his mysterious origins and vaporized both of them. By then, Ayla had already fled, so she didn't realize. He was about to follow, but tripped over a rock on the cliff and fell down, landing in the sea. Days later, he washed up to shore, with no memories. He was found by a prehistoric aardvark who cared for him over the next few days, until he was strong enough to go find his memories again.
Upon setting out into the mountains to the east of Singing Mountain, he came upon an advanced version Time Egg which had been dropped by a time traveler from 19,205 AD - by then every biological being had been integrated into FATE in this Keystone timeline. FATE from 19,205 AD altered the mechanics of this Egg slightly so that when Kino touched it, he would be transported to 15,000 AD to be used by FATE to prevent an incident involving certain highly powerful artifacts under the control of DESTINY, a rival computer of temporal control constructed by FATE's opponents in that era in a subplot entirely irrelevant to the Chrono series. However, under this timeline, due to certain actions of Kino, he caused a young time traveler from 15,000 AD to go back in time and accidentally prevent the Prometheus Circuit from being destroyed and in fact causing it to exercise far greater restraint over FATE, thus causing DESTINY to destroy FATE in 15,001 AD.
To reward Kino, DESTINY grants him one wish, which the computer would be able to grant due to its unrestricted hegemony over all of time-space now. Kino wants to regain his memories, and so DESTINY alters the timeline so that Kino does not hit is head upon falling off the cliff, then creates a gate to 15,001 AD where he fell - this new version of Kino succeeds the old one by TB. Having regained his memories, Kino asks DESTINY to return him to his own time, but DESTINY refuses. Kino is enraged, but pretends that he is only mildly disappointed.
Over the next decade, Kino begins a human resistance against DESTINY's rule, culminating in the use of background radiation from the very edge of the observable universe to disrupt DESTINY's time-probing abilities - in the resulting confusion, the last aspect of the computer's interface is destroyed, and all copies are corrupted. With DESTINY out of the way, Kino's resistance breaks into the central physical fortress of the humans under DESTINY's sway and help him use the time machine to return to his time.
Needless to say, he discovers he no longer can live comfortably in such a primitive environment after only a week in the southern village he arrived at, and so becomes angry and bitter at the world. He decides to wander as a hermit for the rest of his life - but when he goes to the mountain where he was found as a child, he discovers a gate. When he goes through it, he discovers his origin - he was a lost child from a futuristic Zeal-esque society imbued with natural magic, kidnapped and placed there by the computer which replaces DESTINY in 20,000 AD - ANOTHERPSEUDOSYNONYMOFDETERMINISTICFUTURE simply so that he could engineer both FATE and DESTINY's downfall, giving ANOTHERPSEUDOSYNONYMOFDETERMINISTICFUTURE complete rule over space-time. Knowing now that all his life he has been a pawn, he begins discreetly gathering power and building supercomputers of his own. When he senses the disturbance to the Frozen Flame resulting from the events you have seen in Crimson Echoes, he travels there using the incomprehensibly advanced technology he has developed using his inhuman skills, replaces the Frozen Flame with a copy, and steals the real Frozen Flame to further increase his own power.
He does similar things with other sources of magical energy throughout time, until ANOTHERPSEUDOSYNONYMOFDETERMINISTICFUTURE becomes aware of him. It sends agents to destroy him or erase him from the timeline, but he has become immune to all such aspects of space-time - his very existence is outside of time now. He still can be killed like a mortal - he has not subverted that weakness yet, but magic is harmless against him, and his technological wonders easily can destroy any would-be assassins. Kino himself appears in 20,000 AD and destroys ANOTHERPSEUDOSYNONYMOFDETERMINISTICFUTURE - "travels to" would have been an incorrect term, as he is outside the timeline.
Finally, he decides to confront the party, his once-friends, in Chronopolis: He wants to make them suffer for everything that he has gone through. He then plans to destroy all of space-time. He does not realize they had nothing to do with it; he is half-crazed, inhuman now. He appears in Chronopolis and using his god-like powers, makes the entire party and everyone present writhe in agony.
But then, he accidentally trips and falls into the ocean, and drowns from sheer surprise that he could still trip. Everything he ever did and every effect he had on the timeline is erased due to the fact that he had removed himself from the timeline.
