WARNING: SPOILTERS AHEAD
Magus is a powerful sorcerer from the Dark Ages. He is a master of shadow magic, and is also well versed with the other elements. When he is unable to use his magic, a scythe is his weapon of choice
Magus's true name is Janus, Prince of Zeal. He is the son of Queen Zeal, and brother to Princess Schala. He was a child during the construction of the Undersea Palace and the Mammon Machine. He was present during the activation, and stood witness as Lavos was summoned. Lavos created a series of gates, one of which Janus fell into. When he awoke, he was surrounded by Ozzie and the Mystics in the Middle Ages.
After demonstrating his power to the Mystics, and being chosen as their leader, Magus declares war upon the humans. This is merely a ploy, however, as his true goal was to summon Lavos. His plan was to call forth the entity, and kill it, as revenge for the destruction of Zeal.
This plan was interrupted, however, by Crono and his friends. They barged in on Magus in the middle of the summoning, and forced Magus to devote some of his attention to them. Magus still managed to call Lavos, who again opened a variety of gates, sending Magus back into the Dark Ages.
Many years older then when he left, Magus returned to Zeal but was unrecognized even by his own family. He took up the guise of a prophet, and used his knowledge of the events that would happen to gain the Queen's trust.
He used his influence to again be present when the Mammon Machine was activated. Crono and his posse arrived at the same time, to do battle with Lavos. However, Lavos killed Crono, and Magus was unable to defeat the beast alone. Just in the nick of time, Schala transported the group away from the destruction.
Magus climbed up North Cape to watch the destruction of the world. Frog follows, and confronts him. Instead of a conflict, though, an uneasy alliance is formed between the two, with the goal of defeating Lavos.