After taking Troy and sailing to Greece for repairs, they stumble on a plot by Gargarensis, a cyclops demigod who is trying to help a god release Kronos from Tartarus. That is, until Atlantis is attacked by strange monsters and men in black ships, prompting Arkantos to go off to Troy and help Agamemnon finish The Trojan War to curry favor with Poseidon. The plot of the original game follows Arkantos, an Atlantean Admiral who battled monsters in his time but is getting old, and since no one's really attacking Atlantis, he doesn't have much to do.

Also, while it shared some Tropes with Age of Empires, it contained many which weren't applicable to the mother series. Rather, it was based in ancient Earth, where there were real Gods and play as three civilizations based on their various mythologies, and followed consistent, original storylines through characters and in-game cinematics. It had similar town-building structure and similar units, but veered away from the traditional realism of the Age of Empires series. Age of Mythology is a spin-off from the Age of Empires series.

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