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During development, Ayla's animations sported bouncier breasts, but this facet of her animations was toned down before release.
Contributed by ProtoSnake
For video game magazine Game Informer's issue featuring their review for Chrono Trigger, they were planning to include a full cover spread featuring exclusive custom Chrono Trigger artwork by the game's artist, Akira Toriyama. Despite the game's publisher, Square Enix, agreeing on it, a week before it was to be made they informed Game Informer that Toriyama had decided not to do it in fear that due to his drawings being worth a lot they will most likely be sold on the black market. Lunar: The Silver Star was featured on Game Informer's cover instead.
Contributed by KnowledgeBase
There is a cut location called Singing Mountain that was originally going to appear in the Prehistoric era. It also includes an unused song sharing the same name. The dungeon and accompanying song ended up being cut because the dungeon itself didn't contain much, nor did it advance the story.
Contributed by G-Haven
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The chest behind the counter in Truce Inn contains 57,342G. The chest can't be reached without cheating, and was likely only used for debugging purposes.
Contributed by Mawille
Massato Kato stated in a Chrono Trigger Ultimania interview that he and Yuji Horii intended for Crono Spoiler:to stay dead after the Ocean Palace scenario. The party would have to then retrieve a version of Crono pre-dating the Millennial Fair to complete the quest, and then return him to his home time, Spoiler:bitter-sweetly knowing he would go on to die at the Ocean Palace. Square deemed this too depressing and had them write the clone plot device to save him.
Contributed by Cavery210
Two soldiers called Vicks/Biggs and Wedge appear in Chrono Trigger, as employees in Norstein Bekkler's Tent of Horrors. This a reference to both Star Wars and Final Fantasy VI. A V-Jump issue in Japan humorously state that after Tritoch made them disappear in Final Fantasy VI, they ended up in the Chrono Trigger dimension and were found by Norstein, who gave them their new jobs.
Contributed by Cavery210
In the FMV of the PlayStation and DS releases, Robo is the only playable character without a special ending.
Contributed by Psychospacecow
In the Japanese version, Robo has a unique speech; he speaks with bits of katakana in his sayings and has trouble with pronunciations. Most of the robots talk in all katakana, with the exception of Johnny.
Contributed by Psychospacecow
Despite his gigantic outward appearance and the scope of his power, the core of Lavos is surprisingly miniscule. In the final battle the player is led to believe the center creature is the core, but the true core is actually on the right, mirroring the appearance of the left Lavos Pod. It will continue to revive the center and left Pods until the Core itself is defeated.
Contributed by TomGuycott
In the North American version, the three bosses that you fight in Ozzie's tower are named after famous musicians. these are Ozzy Osbourne from Black Sabbath, Slash from Guns n Roses, and Flea from Red Hot Chili Peppers. There is even an NPC that states "they're tone-deaf, evil fiends."

Ozzie, Slash, and Flea's Japanese name's are, respectively, Vinegar, Soysau (Soy Sauce), and Mayonnai (Mayonnaise).
Contributed by gamemaster1991
Norstein Bekkler's laugh is the same as Kefka Palazzo's laugh from Final Fantasy 6.
Contributed by Chronowarhead
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After beating the game you have the option to replay using everything you acquired through your first play through. Using this to beat the game's main villain at the very beginning of the game will unlock a secret ending where you meet the game's developers at the End of Time.
Contributed by Berry
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There have been two non-profit fangames which received a substantial amount of coverage that were ultimately shutdown by SquareEnix.

The first was Chrono Resurrection, a 3D remake of the original for PC, Xbox, Gamecube and the Nintendo 64. The second was Chrono Trigger: Crimson Echoes, a ROM hack of the original game which served as a sequel set five years after.

Both projects were stopped in 2004 and 2009 respectively, after receiving a cease and desist letter from SquareEnix. An alpha version of Crimson Echoes has since been leaked online.
Contributed by KnowledgeBase