Legacy of Cyrus is a novelty mode focusing on the parts of the game involving Frog and Magus. This type of run originated with Taco Hero's “Medina Redeemed” and Proccy's “Frog Hell Seed” runs. The current rules and recommended flags were designed by Cthulhu Crisis.

To complete a Legacy of Cyrus game you must perform the following tasks in order:

1. Repair the Northern Ruins (requires Grand Leon, Frog, Magus) and interact with Cyrus's grave with Frog.
2. Open the Magic Cave (requires Melchior repairing the Masamune with the Bent Hilt and Bent Sword) and defeat Magus at the end of Magus's castle.
3. Defeat Ozzie at the end of Ozzie's fort. The run officially ends when the cat hits the switch to drop Ozzie.

The above order is enforced by the game, but other checks can be performed at any time. In particular, both Magus and Frog must be recruited prior to turning in the Grand Leon to the carpenter to repair the Northern Ruins. The game will also lock Magus and Frog into the party once they are recruited.

Since Legacy of Cyrus focuses on the above dungeons, the following modifications have been made to streamline the experience.

• Access to Future has been removed (Access to Mt. Woe via the Gate Key is still possible).
• Useless Key Items (like Moon Stone, Chrono Trigger, Ruby Knife, etc) will be replaced by high tier gear drops.
• Removal of the future means that one character is inaccessible.
  • If Robo is rolled in the future, his Ribbon is removed from the Key Item pool. If Marle is rolled in the future, the Prism Shard is removed.
  • The boss Magus at the end of Magus's Castle will always roll as the character who is inaccessible.
• An ending has been added after Ozzie's Fort.
• Defeating Magus does NOT open the zeal palace door, and the message is changed so you know you need to go to Ozzie.
• If the early pendant (p flag) is on, the Pendant, when found, is instantly charged and can be used to open sealed chests in 600AD/1000AD.

The following flags are not forced by the randomizer, but Cthulhu Crisis considers them to be the official flags of the mode:

• (n) Normal difficulty
• (g) Glitches disabled
• (z) Zeal 2 acts as final boss (she won't be engaged in a LoC run)
• (p) Early pendant charge (no need to visit Mammon Machine)
• (m) Magic is unlocked without visiting Spekkio
• (q) Gear Randomization
• (te) Fully random tech order