For future reference, I'll provide a rationale for my choices.
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The Fool - Chrono. The Fool represents the querent. He is the protagonist of the journey, striking out boldly into the unknown. Likewise, Chrono is the avatar of the player. He doesn't hesitate to leap into the unknown and take on challenges, even if this turns out to be unwise. We considered making the Player the Fool (and Chrono the Magician), but I think Chrono is enough of an avatar that it works. Besides, Chrono's character is a better fit for the Fool, with his potential, courage, and (at times) recklessness.
The Magician - Norstein Bekkler. The Magician uses creative energy to unlock potential and make things manifest. Chrono could fit here, but Norstein Bekkler is a better choice. He plays the part, and he creates the clone which is vital for bringing back Chrono. His ability to manifest something as strange as a clone, his power to solve the party's dilemma, and his role in resurrection all point to the Magician. This is especially true because the Magician acts as a conduit between the heavens and the earth, and Chrono's resurrection alludes to this.
High Priestess - Schala. The High Priestess represents female divinity, the esoteric, and intuition. Schala certainly looks the part, she has great magical power, and she's enigmatic. She is directly connected to Magus' mysterious past, and her fate is one of the few loose threads at the end of the game.
Empress - Queen Leene. The Empress represents growth and nurturing of life. Queen Leene fits this role, especially since she is key to continuing the Guardian royal line.
Emperor - Azala. The Emperor represents male authority, order, rule of law, discipline, and power. Likewise, Azala is absolute ruler of the Reptites; capable of constructing fortresses, leading armies, controlling a Tyrannosaur, and governing her race. Her ability to enforce order on primal strength makes her an almost ideal fit. The one problem is that Azala is female, while the Emperor is male. However, this one contradiction can be permitted, since in all other regards she is definitely an authoritarian Emperor. She is certainly not a nurturing Empress, especially since her race went extinct.
Hierophant - Gaspar. It took me a long time to make this connection, but it is the correct choice (and it finally unraveled the Guru knot). The Hierophant represents spiritual leadership and communal traditions. While Gaspar looks like a Hermit, in fact he plays the Hierophant role to the hilt. He presides over the End of Time, which is a home base for your party. Throughout the game, he provides leadership, guidance, and information on what is happening and what to do next. He is the spiritual leader of the party, thus the Hierophant.
Lovers - Chrono & Marle. The Lovers is about relationships and desire. The whole adventure begins with a chance encounter between Chrono & Marle, Chrono risking himself to save her, and Marle defending his innocence. Throughout the story, we are given strong hints that there is chemistry between the two. They're not the only relationship -- there's also Lucca/Robo, Magus/Schala, Ayla/Kino etc. -- but theirs is the most prominent.
Chariot - Epoch. The Chariot is about motivation, decisiveness, and achieving victory. The fact that it is a vehicle is an obvious parallel with the Epoch, but there is more. The Epoch overcomes the obstacle of the sealed gate to continue your adventure, and it can crash right through Lavos' shell. Likewise, the Chariot can run over obstacles and break enemy ranks. The enhanced ability to travel through time and space fits well with ambition and energy of the Chariot.
Strength - Ayla. Strength, also known as Fortitude, is about taming one's primal energy and passions. By tapping into that raw energy in a disciplined way, you can get much more out of it. Ayla is primal energy par excellence, but she's not completely wild and out of control. She combines her raw power with discipline, morals, and a philosophical outlook. This can be seen at many points, such as her punishment of Kino, her leadership of the Iokans, and her frank views on the human/reptite conflict: "Win and live. Lose and die. Rule of life. No change rule." which is one of the best quotes from the game.
Hermit - Belthasar. The Hermit is about withdrawal from society, pondering, reflecting, and eventually re-emerging with new insights. Likewise, Belthasar lives a solitary life in the bleak future, with only a cybernetic Nu for company. While you can meet him in person, you cannot get much out of him. It is only later, after he succumbs to madness and/or death, that the party can reap the rewards of his solitary work and research (the Epoch, Poyozo dolls, insights into Lavos, etc.)
Wheel of Fortune - Time Gate. The Wheel of Fortune is all about luck and change. Likewise, the Time Gates send you on your adventure, and you have no idea when and where you'll end up. The card has several figures around the wheel, which should be replaced by the iconic characters I mentioned.
Justice - Frog. Justice is about fairness and impartiality. It's also about making painful adjustments to right wrongs and restore balance. Frog represents chivalry and fights for what is right. More importantly, he makes the difficult decision to let go of all his regrets, rejoin the party, fight Magus, and eventually make peace with Cyrus -- this definitely fits with making difficult adjustments to set things right. Frog wields the Masamune/Grandleon, and this is another powerful connection to Justice. The Masamune tests you in battle to see if you are worthy of it, regardless of who you are. And of course, there's that famous line -- "it's not who owns the sword, it's how you use it" which is concurrent with the concept of Justice.
Hanged Man - Robo. The Hanged Man is a card of introspection, inversion, suspension, and epiphany. It is about one's perspective being dramatically altered. Robo fits this to a T. When he is first activated, he is asked what he wants to do, and this comes as a shock to Robo. He spent his entire pre-1999 existence carrying out orders and following programming. Suddenly, his world is toppled, and he is in the paradoxical situation of being a robot with free will. He chooses to join the party as an assertion of his new identity. He breaks free of his old programming, even though he is viciously attacked by the R series and Mother Brain for doing so; likewise, the hanged man has an inverted perspective compared to everyone else who is upright. Another example is the Fiona's Forest sidequest. Robo spends centuries growing the forest, and is found in stasis in the shrine. He is suspended in limbo during this stretch of time, and this gives him unprecedented insights into the Entity.
Death - Lavos. Death is misunderstood. Yes, it can mean death and destruction, but it can also have the meaning of 'destroy and rebuild'. One has to burn away the dead wood so new shoots can grow. That's why I insist that this card not depict 1999 and its all-out destruction of the world. Instead, it should depict Lavos' fall in prehistory, or his intentional destruction of Zeal. In both of those cases, one way of life & civilization had to fall so a new one could take its place. The Reptites were destroyed so that humans could inherit the earth. Zeal was destroyed so the modern world could take its place. In either case, there is an ending which leads to a new beginning. Since Lavos plays this role in the world's history, he should be the Death card, notwithstanding the fact that Lavos is the villain and Death is not necessarily evil.
Temperance - Melchior. Temperance is about moderation and combining opposites to achieve synthesis. Melchior is a renowned smith of weapons and armor. There's also the juxtaposition between the fact that he's the Guru of Life, yet he makes weapons and equipment for battle. However, if you use weapons for the right cause, you can defend life, which is a synthesis between seeming opposites. His repair of the Masamune/Grandleon is another example of synthesis through careful work and the right proportions.
Devil - Magus. The Devil is another misunderstood card. He's not about being evil -- rather, he's about losing restraint, going to extremes, giving in to excess. The Devil is about power, carnal desire, and so on. Likewise, Magus seems like an evil villain at first, but he's more of an antihero. He leads the Mystics because he wants power, and he'll go to any extreme to save Schala and defeat Lavos -- even if that means joining the party who tried to destroy him. Magus' power, unorthodox methods, and extreme choices clearly identify him as the Devil. Besides, they match on an intuitive level.
Tower - Mammon Machine. The Tower is about tearing down falsehoods and punishing hubris. It is a dramatic downfall for overreaching arrogance and lies. The Mammon Machine is an ideal fit here. The Zealians deluded themselves into believing that living off of Lavos' power was a sustainable path. They were already on top of the world, and tried to siphon off even more power from Lavos in an attempt to attain immortality. For this overreaching hubris, their entire civilization was destroyed. The Mammon Machine, and the fall of Zeal in general, reflects the Tower.
Star - Marle w/ Pendant. The Star is a symbol of hope and guidance. Things may not be good now, but there is potential for the future. As long as you stay on the path, there will be help along the way. The pendant is the trigger that starts the whole adventure, and it becomes a boon later on, opening doors that previously blocked your path. It's like a guiding light, which is why it fits as the Star.
Moon - Dreamstone. The Moon represents the subconscious, imagination, intuition, the world of dreams, visions, and nightmares. Likewise, dreamstone has strange, enigmatic qualities. It can harness and store magical energy, including that of Lavos. It was used to forge the Masamune/Grandleon and the Pendant, but also the Mammon Machine. There's also that text in Zeal that describes the "strange red rock" with "powers beyond human comprehension" which created love and hate (implying that it caused humans to evolve or gain knowledge, like the pomegranates of the Garden of Eden). A substance with such dangerous power fits well with the Moon. I'd recommend Queen Zeal's reflection in the stone, so that 1) she gets referenced in the Major Arcana, and 2) to hint at the dark side or "lunacy" of the Moon.
Sun - Lucca. The Sun is about science, reason, clarity, and optimism -- the opposite of the Moon. Lucca has a strong affinity for science, technology, and reason. She is the mastermind of the party, and approaches problems with vigor and intellect. She is an ideal fit. In addition, the card could include the Sun Stone, or maybe the Wondershot charging up a bright ball of energy.
Judgment - Chrono Trigger. Judgment is about forgiveness, making amends, moving on from the past, resurrection and healing. The Chrono Trigger/Time Egg is a perfect fit for this. It brings you back to the lowest point, and allows you to change things for the better. Once Chrono is back, the party can finally move forward and complete their quest. There is also a literal sense of judgment in that you must earn the Chrono Trigger's intercession by putting in the effort (getting the clone, climbing death peak, etc.) to prove your dedication.
World - Nu/Entity. The World is about the universe, of course. It's also about completion and coming full circle. The Entity, the spirit of the planet, fits with this, as does the Nu. In particular, there is the famous line: "All life begins with Nu and ends with Nu." That sense of alpha and omega, the complete circle, fits well with the World card. There are also figures in the corner, representing the varied aspects and qualities of the universe. For Chrono Tarot, I chose representatives of four major cultures from different eras: guardian soldier, reptite, mystic imp, and enlightened one.
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A final note about the Major Arcana: we wanted to fit all 7 party members and all 3 gurus, while still making selections that suited the meaning and style of each. The difficulty of this is what I mean by the "guru knot". Assigning Gaspar to Hierophant was the breakthrough.
As for the Minor Arcana, I won't discuss it in detail now. I will mention the qualities of the suits:
Swords: air, intellect, debate, nobility/military
Wands: fire, energy, ambition, creativity
Cups: water, emotion, faith, love
Pentacles: earth, body, possessions, wealth
Aces represent each suit in its quintessential form. The court cards are self-explanatory.
From this, hopefully you can see the logic behind all the choices I made. I strove for some amount of moral balance -- Janus as page of cups makes that suit a little darker, while Masa & Mune bring a positive note to Swords. I debated a bit over Queen of Swords and Queen of Wands, but the correct choices became clear: the power and ambition of Queen Zeal fits Wands; the militancy, logic, and persuasiveness of Mother Brain fits Swords.