The Magic Cave has two entrances, one on the Southwestern continent (east of Fiona's Villa) and the Central continent (south of Magus's Lair). The tunnel goes under the water separating the two continents.
After Frog joins Crono's party, they head for the Magic Cave. Using the power of the Masamune, Frog opens the rock entrance to the Cave. They journey through the underground tunnels battling strange monsters and emerge on the central continent, where the only thing that stands is Magus' castle.