Queen Zeal, the malevolent, power-hungry ruler of the Zeal Empire (Babylon) in 12,000 B.C., is parallel in quite a few ways to the Antichrist. The Antichrist is said to be the most evil being who will ever walk the face of the Earth, and will foreshadow the coming of the Apocalypse. This parallel is extremely well-supported, and was most likely intentional.
The Antichrist is said to be a world conqueror, who will subdue or charm most of mankind into submission. Similarly, Queen Zeal has either enslaved mankind through force (the Earthbound Ones, who cannot use magic), or charmed them into following her (the Zeal Empire, who loves her for giving them a paradise to live in).
The Antichrist, while taking control of most of the world, will not conquer all of it. Notice that the Three Gurus of Zeal still do not follow the Queen's orders, thus making her New World Order incomplete.
After subduing most of the world, the Antichrist will turn against mankind and attempt to annihilate it. Similarly, after Queen Zeal completes the Ocean Palace, she forsakes her kingdom and works to raise Lavos so to gain eternal power for herself. She does not care if this destroys all of mankind.
The Antichrist will join forces with the False Prophet in his/her conquest for power. Notice that Queen Zeal works together with the Prophet (really Magus, who, being from far in the future, is not a true prophet). This is directly parallel to the Antichrist and the False Prophet.
The Antichrist is the foreshadow of Armageddon, in which all life on earth ends. During the Apocalypse, a killer comet named Wormwood will fall to Earth and be the ultimate destruction of everything. Similarly, Queen Zeal is the foreshadowing (in The Black Omen) of the coming of Lavos (Wormwood) who is through no coincidence a killer comet that crashes to Earth and destroys everything. Notice that Queen Zeal actually awakens Lavos when she is approached by the main party.
Concerning the relationship of the Antichrist and the False Prophet, they both share the same origin: a beast of incredible power that comes screaming out of the depths of the abyss. Similarly, Queen Zeal and Magus (the False Prophet) not only both come from the Zeal Empire in 12,000 B.C., but they are also related as mother and son.
When Crono (Jesus) sacrifices his life in the Ocean Palace, it is before Queen Zeal, who, being the Antichrist, represents all the sins of the world rolled into one. This is much like Jesus Christ sacrificing his life for the sins of the world.
During his/her reign, the Antichrist, through the powers of Hell, will create a body replica of Jesus Christ to further decieve mankind with so as to gain their love and support. Notice that in the Black Omen, before battling Queen Zeal, you will pass by a body replica of each member of Crono's (Jesus's) party? Curious, isn't it?
The Antichrist is prophecized to rule the world from the area that was once Babylon. Similarly, Queen Zeal rules the world of 12,000 B.C. from Zeal Empire (Babylon). The Empire is similar to Babylon in that Babylon was an empire that enslaved the Israelites (Earthbound ones), and was eventually destroyed via the wrath of God for worshipping pagan gods and being full of sin (Just as Zeal is destroyed as a result of Queen Zeal's great sins against mankind). Even more connections are listed on Zeal's page.
According to Revelations, the Antichrist will be a horrible beast that emerges from the sea. Notice that Queen Zeal, after summoning Lavos, rises out of the sea in the Ocean Palace (Now the Black Omen) in a dramatic sequence.
There is said to, during the time of the Antichrist, exist a mysterious woman draped in a purple robe who is tempted to become a tool of the Antichrist. This woman is known as Mystery Babylon. This mysterious woman, after becoming situated alongside the Antichrist, will become hated by the Antichrist. Eventually, the Antichrist will "bring her to ruin, leave her naked, eat her flesh, and burn her with fire". This mysterious woman in purple is none other than Schala, Queen Zeal's daughter. Through the game, Schala is used up as a tool of Queen Zeal. Her powers are exploited and raped for all they are worth (thus, her flesh is eaten by the Antichrist, and she is left naked). Finally, when she is of no more use to her mother, Queen Zeal crushes her (she is brought to ruin, and burned with fire). Also...notice that Schala is draped in a purple robe. Coincidence? I doubt it.