Moving on to Magus's role as the False Prophet, note above that Queen Zeal is the final incarnation of the Antichrist before the Apocalypse. The Antichrist is said to work side by side with the False Prophet, a being who appears to know the future and create great miracles to decieve the public into worshipping both himself and the Antichrist. Well, in Chrono Trigger, Magus returns to Zeal Palace (12,600 years before his time) under the guise of the Prophet. As the Prophet, Magus goes around foretelling the future with 100% accuracy, becuase he is from the future and knows history. Thus, he is not really seeing into the future. Hence, the False Prophet. As the Prophet, Magus aids Queen Zeal (just as the False Prophet aids the Antichrist) in achieving her goals (though he's really just using her to achieve his own goals).
The False Prophet and the Antichrist are said to be of the same origin: both beasts of incredible power who come screaming out of the depths of the abyss. This is similar to Magus (the False Prophet) and Queen Zeal (the Antichrist) being so closely related as mother and son, and both coming from the Kingdom of Zeal.
Now moving on to Magus's role as Janus, the Greek god of gates and doorways. Janus was a god who had two faces, both always facing in opposite directions. This is similar to Magus being a foe for one half of the game, and an ally for the other half. His position towards the main party is split in two different directions.