Lavos, the alien being that falls from the sky in shape of a comet and brings about its destruction, is quite similar to Wormwood. Wormwood is the name of a comet in the Book of Revelations that crashes to Earth during the Apocalypse and destroys everything. This parallel is brief, yet powerful.
After the coming of the Antichrist, who foreshadows the Apocalypse, Wormwood comes crashing down to earth and terminates all life. Similarly, after Queen Zeal (the Antichrist) attempts to become God by using the power of Lavos, she winds up awakening Lavos from its eon-long slumber to destroy the world.
Wormwood is a comet that destroys Earth. Lavos is a comet that destroys the Chrono Trigger world.
The year often associated with the Apocalypse is 1999 A.D.--exactly the date of the Apocalypse in Chrono Trigger.