Ozzie, known in the Japanese version of the game as Vinegar (ビネガー, Binegā?), is a rather fat and large Mystic. From the events provided, Ozzie raised Janus and developed his magical skills. However, Janus soon became too powerful for even the great Ozzie to handle and the roles were switched: Janus became Magus and the new leader of the Mystics. Ozzie remained loyal as a war started against the Kingdom of Guardia and the human race. He continued to retain a position of power as Magus' top general. The player must fight Ozzie during the battle of Zenan Bridge and in Magus' castle. Ozzie is encountered a third time in an optional side quest as he hides in his fort. Here, he is equipped with Ozzie's Pants which are worn on the head and calls himself “Great Ozzie”. With Flea and Slash still working for him, the trio engage in an ultimate battle against the heroes.

In Chrono Cross, Ozzie is shown wearing purple armor and pants. He also wears an orange mohawk and beard.

Slash, known in the Japanese version of the game as Soysau (ソイソー, Soisō?), is a tall and lanky Mystic with an obsession with swords. He is considered a great swordsman, and is very pleased with the opportunity to fight Crono and Frog when they arrive at Magus' castle. With his failure to defend Magus' castle against the heroes, Slash is provided a new sword, the Slasher 2, and changes his name to Super Slash. He was defeated in the battle of the 3 Mystics against the heroes at Ozzie's Fort. In the Japanese version, Slash is more respectful and honorable in his speech.

In Chrono Cross, Slash is clean-shaven and sports a queue. He wears identical clothes, although they are blue.

Flea, known in the Japanese version of the game as Mayonnai (マヨネー, Mayonē?), appears to be a humanoid female (ample breasts and hourglass figure), but reveals that he is actually a man. Flea has the ability of transforming into a bat and actually follows the heroes around the castle since the Magic Cave before eventually showing his true colors and coming out. He is defeated by the heroes in their first confrontation. As expected, Flea joins Ozzie and Slash in Ozzie's fort. He now has the Flea Vest (a bra in the Japanese version) and is now named Flea Plus. With a few upgrades to his magical arsenal, Flea prepares himself again to battle it out; however, he is defeated.

In Chrono Cross, Flea has undergone the most physical changes of the Mystic trio. He has a medium-length haircut parted in the middle and a sailor-like shirt instead of a bustier. The description of the “Flea Vest” states that it “makes him look feminine.”

Schala (サラ, Sara?) is the daughter of Queen Zeal and the older sister of Janus. She was raised in the Kingdom of Zeal in 12000 B.C., when mankind was separated between the Enlightened Ones, who are able to use magic, and the Earthbound Ones, who are not. She is one of the few Enlightened Ones sympathetic towards the Earthbound Ones. Schala was forced by her power-hungry mother, Queen Zeal, to use her magic powers in order to try and control the energy of Lavos with the Mammon Machine. Although an NPC, Schala's later disappearance from the story line surprised fans. Two years before the Final Fantasy VII Aerith Gainsborough rumour, Schala received similar infamy with players on a quest to relocate her. Examination of a beta version of the game eventually ruled out any possibility that Schala was planned as a playable character in the final stages of the game.

In Radical Dreamers, Schala's fate is explained as she is seen reincarnated as Kid. In the other sequel Chrono Cross, which essentially retcons the events of Radical Dreamers, it is shown instead that Schala was thrown into the Darkness of Time after the kingdom's destruction. She was later fused into the defeated Lavos and the two eventually evolved into the Time Devourer. But Schala, trying to fight the Time Devourer's influence, sent her daughter/clone Kid to Lucca. Serge, the main character of Chrono Cross, must defeat the Time Devourer and set Schala free with the Chrono Cross. Interestingly, Schala's hair is blonde in both Radical Dreamers and Chrono Cross in contrast with the blue hair from Chrono Trigger. Some fans have suggested that the Enlightened Ones dye their hair blue to further distinguish them from the Earthbound Ones.

The Guru of Life Melchior, the Guru of Time Gaspar, and the Guru of Reason Belthasar, are three figures of authority originally living in the Kingdom of Zeal in 12000 B.C. Their original Japanese names are Gasch (ガッシュ, Gasshu?), Hash (ハッシュ, Hasshu?), and Bosch (ボッシュ, Bosshu?). They served as wise men and advisors to Queen Zeal and were among the few Enlightened Ones who did not look down on the Earthbound Ones. When Queen Zeal became obsessed with harnessing the energy of Lavos, the Gurus tried to stop her, which ultimately resulted in Lavos sending each of them into different eras of the future: Melchior to 1000 A.D., Belthasar to 2300 A.D., and Gaspar to the End of Time. It is in their respective eras that the player encounters them and receives valuable items and advice from them.

In Chrono Cross, Belthasar is alive and well, due to the changed future. By 2300 A.D. of the new future, the world's society has reached hypertechnology levels and Belthasar founds the military time research facility, Chronopolis. With this done, he begins to initiate “Project Kid”, which is an unusually complicated series of events requiring the birth and participation of a boy named Serge to rescue Princess Schala, who had been missing since the Fall of Zeal, and ultimately leading to the annihilation of the Devourer of Time, thus saving the universe. Naturally, he reveals himself to Serge twice over the course of the game and rather cryptically, reveals what his true purpose is.

Early in the game, the characters believe that Lavos created the time Gates. However, the “Green Dream” event near the end of the game offers an alternate explanation: due to the timing of when the gates appeared and their significance, the gates may have been created by some other entity reliving its life cycle, and flashing back over important memories in its past which were tied to Lavos. Since the existence of one of the gates predated Lavos's arrival on Earth, and all the time periods visited were related in some way to Lavos's effects on the planet, the gates could have appeared as a result of some entity reliving its life before the world perished, the entity most likely being the planet itself (this is suggested far more heavily in the Japanese version, as are all references to the planet being alive). The gates disappeared after Lavos was defeated, suggesting that the entity was at peace or that Lavos's influence no longer affected the space-time continuum.

Lavos (ラヴォス, Ravosu?) is Chrono Trigger's primary villain, and is an alien parasite that crash landed in the year 65,000,000 B.C. and was named by Ayla (“La” meaning “fire” and “Vos” “big” in an ancient language). Lavos came to Earth with the intention of draining its energy so that it could produce genetically enhanced spawn, which would then continue the cycle on other planets. In the North American version of the game, it is claimed once in the series that Lavos directly influenced all technology and life on the planet, evolving the planet's life forms to cultivate it, and make itself stronger. However, the line is absent in the Japanese version. In the original timeline, Lavos slept for millions of years, gaining power until 1999 A.D., when he emerged and put the world into an apocalyptic state. However, because of the interference of many of the characters, he was summoned at two other points in time - 12000 B.C. and 600 A.D. While traveling in 2300 A.D., Crono, Marle, and Lucca see a video of the Day of Lavos which occurred in 1999 A.D., and decide to prevent it somehow. Magus is also after Lavos for destroying his home era of 12000 B.C.

In the final battle between the heroes and Lavos in Chrono Trigger, Lavos has three different forms. The first form is the outer shell. It is possible to skip the entire outer shell by using the Epoch to smash through Lavos's shell, resulting in a different ending. Once the party defeats the outer shell, the party members go inside to fight a second form, which has a body and two arms. Defeating the two arms shuts off the main body defense, allowing the party to defeat it. The third and final battle of the game is against Lavos Core. Lavos Core consists of three parts: a humanoid center, and two bits. In order to defeat Lavos, the party must defeat the right bit. Once the Lavos Core is defeated, the game finishes, and one of the multiple ends is shown.

While the natural “dreamstone” is a substance responsible for the first evolution of human beings from animal apes to sentient creatures, it is revealed in Chrono Cross that Lavos is responsible for the creation and advancement of the actual modern human species. Upon impact, a splinter of Lavos's shell broke off. This becomes the focal point of Chrono Cross, the Frozen Flame. Lavos is also the final boss in Chrono Cross, except in the form of the Devourer of Time, the result of the defeated Lavos assimilating Schala in the darkness beyond time.

zala (アザーラ, Azāra?) is the leader of the Reptites from 65,000,000 B.C. who lead the effort to destroy the human race to prove their superiority. Refers to humans as “apes”. Interestingly, Azala's gender is never stated once in the entire game. He supposedly dies from the impact of Lavos crashing into the Tyrano Lair.

Cyrus (サイラス, Sairasu?) is a hero from 590 A.D. He was the Commander of the Knights of the Square Table, who was defeated and subsequently killed by Magus even with the legendary Masamune at his possession. One technique at his disposal was “Nirvana Strike,” which he used upon the Frog King in his goal to reclaim the Hero's Medal. His friend, Glenn, was turned into a frog. Later, he appears as an unrestful spirit which Frog must settle down.

Doan (ドン, Don?, Don) is a surviving descendant of the chief of the Information Center from 1999 A.D. In 2300 A.D. the Information Center has become a ruin and is called “Arris Dome”. He is the leader of the few humans living there. In the end of the game, he is revealed to be a descendant of Marle.

Fiona (フィオナ, Fiona?) is a woman from 600 A.D. who replants a forest in the desert using a magic seedling and cared for the land. Robo helps her accomplish this great task, notably after her death over a period of 400 years.

Johnny (ジョニー, Jonī?) “the man” is a biker robot and leader of a gang in Lab 32 of 2300 A.D. He can alternate between a bipedal robot and a “tricycle” like vehicle. In Chrono Cross, the remains of his corpse can be found on one of the highways in the Dead Sea.

Atropos XR (アトロポス, Atoroposu?) is a robot of the R-series and Robo's “girlfriend”, later brainwashed by Mother Brain into killing humans. She appears at the main ending with Robo watching the Epoch.

Dalton (ダルトン, Daruton?) is an ambitious assistant of Queen Zeal who would like to see himself as the new king. He is a golem master and summons several Golems during the game. He is one of the few that survives the Ocean Palace disaster. He commands the huge airplane, the Blackbird. He steals the team's Epoch after the disaster and converts it into an airship. He disappears in the portal that was supposed to summon the Golem Boss. Dalton acts as a high-ranking advisor or general of the magical Kingdom of Zeal, and a member of Queen Zeal’s court.

King Guardia XXI and King Guardia XXXIII (ガルディア, Garudia?) are the kings of the land in 600 A.D. and 1000 A.D., respectively. King Guardia XXXIII and his daughter Marle (aka Princess Nadia) have a strained relationship, though the relationship is patched up during the quest of the Rainbow Shell.

Kino (キーノ, Kīno?) is Ayla's boyfriend and second-in-command of the Ioka tribe.

Masa and Mune, known in Japan as Grand (グラン, Guran?) and Leon (リオン, Rion?), are twin beings of extreme power; fought separately at first, and then fused together. Originally from the Kingdom of Zeal in 12000 B.C., they dwell in the Denadoro Mountains in 600 A.D. and declare themselves protectors of the Masamune. In actuality, they compose the Masamune, which can be reforged by its original creator, the Guru Melchior. The Masamune sword is a recurring reference in many Square videogames to the Japanese swordsmith Masamune. Masa and Mune are known as “Grand” and “Leon” in the Japanese version creating the sword “Grandleon.” They have a “big sister” named Doreen, who has a liking for dreams. This could possibly be because the three are said to be “the embodiment of Melchior's dreams.”

MotherBrain (マザーブレーン, Mazāburēn?) is the head computer of the R-Series manufacturing factory, she desires a utopia of robots after the apocalyptic “Day of Lavos”. She does this by killing the remaining humans of Earth in a human processing plant. She is shut down permanently by Robo and whoever else is in the player's team.

Nu (ヌゥ, Nu?) are sleepy creatures that can be found in all time periods besides 1999 A.D. Nus are blue, with long, stringy arms, small eyes, and a small tuft of green hair. More Nus are found in 12,000 B.C. than in any other era, almost always sleeping. Within a secret room in Enhasa, a book entitled “The Mystery of Life,” vol. 841, chapter 26, authored by Belthasar, states “All life begins with Nu and ends with Nu. This is the truth! This is my belief! …At least for now.” At the End of Time, the final form of Spekkio, the magic trainer, is a pink Nu. This Nu is one of the strongest enemies in the game. A Nu also appears as one of two central characters in the Chrono Trigger promotional anime Dimensional Adventure Numa Monjar.

Queen Leene (リーネ, Rīne?) is the queen of Guardia in 600 A.D. When Marle was transported to 600 A.D., she was mistaken for the Queen who had gone missing. This caused the search for Leene to be cancelled, which in turn caused Marle to not exist until history was changed back. She trusts in Frog as her loyal guardian.

Queen Zeal (ジール, Jīru?) is a power-hungry queen from 12000 B.C. who attempted to control Lavos and siphon its energy for her own power. Although the Queen's devotion to her cause throughout the game borders on obsession and insanity, some dialogue in the game suggests that before she learned of Lavos' potential, she was actually a decent person. This is further reflected by Schala's undying daughterly love and by the gurus, who consider her a victim more than an enemy.

Spekkio (スペッキオ, Supekkio?) is the self-proclaimed Master of War who lives at the End of Time. He introduces the art of Magic to Crono and his teammates and will happily fight them at any time to test their skills. Throughout the game, Spekkio grows in strength with the playable characters, changing his form as he does so, and will offer increasingly useful items when each form is beaten.

Tata (タータ, Tāta?, Tarta) is a youth from 600 A.D. who accidentally stumbled upon Frog's Hero Medal when Frog, drunk, dropped it accidentally in a bar. He was mistakenly thought to be the legendary Hero who would defeat the Demon King Magus.

Toma (トマ, Toma?) is an adventurer of 600 A.D. searching for the legendary Rainbow Shell. Died on the March 6th 634. However his ghost shows up briefly in 1000 A.D. to tell them the location of the Rainbow Shell after the crew pours his soda pop on his grave (sake in the Japanese release). Before he departs to heaven, he claims that Crono and his crew are a “riot a minute”, while in the Japanese release he says the sake he drinks with the crew is the best in the world.

Yakra (ヤクラ, Yakura?) is a monster who devised a plot to kidnap Queen Leene in 600 A.D. and tried to take over the real Chancellor's position with a disguise. In 1000 A.D., the Chancellor is once again being impersonated by the 13th generation descendant of Yakra, bent on revenge and on taking over the kingdom in a bloodless coup through accusations and trial of the King.