Planets have a cycle of souls. Souls are born from the planet, and then return to it.Mikoto
A soul in Final Fantasy IX is the incorporeal essence of a person that is born from the planet's crystal and returns there after separating from the mortal body upon their death. A soul is usually invisible to the naked eye, tough some abstractions for it are shown in the game. A soul appears to comprise of or hold the memories accumulated while alive.
The souls of living beings and their physical bodies exist as separate entities, thus allowing one's soul to persist after the demise of one's body, and even for the souls to be given a new body. The reverse can also happen with the creation of "soulless" beings. The souls are the power everyone holds inside, able to enter Trance, empowering the person to supernatural level.
Crystals reside at the centers of planets and are the source of all life; life is born from them, and souls return to them upon death. As the memories of living beings accumulate inside the crystals, the planets grow; thus the living beings on a planet could be seen as a collective soul for the planet itself, similar to the concept of a lifestream in the Final Fantasy VII series. The crystal gives birth to new life on the planet, thus establishing a cycle of reincarnation. There is no specific plane of afterlife, but one's memories persist after their physical body dies.
Souls can be kept outside a mortal body in stasis, as they exist in Pandemonium. The eye is a common motif that appears in Pandemonium, the underside of the Terran battleship Invincible, and also in the final battle arena , as well as Hades, originally developed as the final boss before being replaced ; the eye motif may represent the souls in stasis observing the living. Another place where souls are kept in stasis is inside the Invincible, which may even use them as a power source akin to Gaians employing Mist-engines, as Kuja claimed the Invincible sucked up the souls to "feed upon them".
Souls that are not inside mortal bodies, the crystal, or held in stasis by some Terran technology like the Pandemonium and the Invincible, may become Mist, the noxious substance that the Iifa Tree expels onto the Mist Continent after having barred them from returning to their crystal. Soulcage claims that Mist is the byproduct of the soul-refinement process. Mist-engines use it as an energy source, and Mist is an ingredient for building black mages. Kuja considers black mages "soulless", but appears to be wrong as they develop distinct personalities and gain the power to enter Trance.
Possible abstractions of souls
Souls are not shown directly, but some abstractions are seen that appear to represent souls. Golden lights appear in a cutscene at the Shimmering Island, rushing through the portal. Zidane calls it "the path that leads the souls to Terra". If the lights represent souls, they may be inspired by the hitodama of Japanese folklore (pyreflies in the Final Fantasy X series are the clearest counterpart to the hitodama in the Final Fantasy series).
The only crystal seen directly is the one in Crystal World, which is surrounded by a blue and a red stream; these may represent the soul cycles akin to Gaia's and Terra's, Gaia being the blue planet, and Terra being the red planet.
An artwork exists of a soul with both Gaian and Terran elements joined together. In it, the soul is simply depicted as a circle. In preparation for the final battle, the party rejuvenate one another; the party members who do not take part, empower those who do seemingly with their own life essences, shown by blue spheres and symbols rising from their bodies and entering the character they are to rejuvenate. This could be an abstraction of a soul.
We must sort the souls. I want to disrupt Gaia's cycle and drain its souls, filling the void with the souls of Terra. To speed the cycle of souls is to speed the work as a whole. Thus, war... And in time... Gaia's souls are gone, and Gaia becomes Terra.Garland
The inhabitants of the ancient planet of Terra pursued immortality, and their souls rested in stasis while their avatar in the world, Garland, put forth the plan to make the young planet of Gaia into a new Terra, whereupon the Terran souls would be given new bodies. Garland constructed "soulless" Genomes at Bran Bal for this purpose.
Garland tampered with Gaia's soul cycle and placed a soul divider around its crystal that stopped the Gaian souls from returning to it, and replaced them with Terran souls, so that Gaia would in time turn into a new Terra. Mist, a malevolent energy that bred monsters, manifested from the refining process. Queen Brahne set up a factory that used the Mist to create black mages, living dolls that Kuja considered soulless.
Zidane, a Genome who unlike most of his brethren was created with a soul, embarked on a journey to save Gaia with the friends he made along the way. Though the black mages and most of the Genomes were considered "soulless", it was implied that the nature of souls was more complex than Garland perhaps understood. Though Vivi Ornitier was a black mage, he was sentient and could enter Trance. His lifespan was fixed, but during his final soliloquy it was implied his memories had returned to the planet, which would mean he had a soul. Garland also tried to remove Zidane's soul to make him into a soulless vessel, but failed. The Genomes at Bran Bal claimed their lives would forever be incomplete if they were not given a soul, and claimed to have no ambitions of their own. Yet, after they moved to Gaia, Mikoto implied that the Genomes had potential to be more than just soulless vessels.
Kuja was another Genome whom Garland created with a soul, and feared losing it, knowing that if Garland's plan was to succeed, he would be discarded and made into a regular Genome. Kuja discovered the world's most powerful force, Trance, the true power of one's soul, from when Mog transformed into the eidolon Madeen. The crystal manifests eidolons out of people's collective imaginings, and Madeen came into being from an earnest wish to protect Eiko Carol. Kuja was unable to enter Trance on his own because he did not live through a childhood and thus was emotionally stunted, but as he was a Genome and thus a soul vessel, he could host others' souls and decided to find a powerful one to allow him to enter Trance.
Kuja took the souls trapped inside the Invincible, and claimed to have used the soul of Queen Brahne as a catalyst to enter a powerful Trance.[note 1] After Kuja killed Garland, the latter remained as an omnipresent voice that guided the party through Memoria, but could not follow them to the Crystal World. After Kuja was defeated, he lost his Trance, and then perished. The results of Garland's plan were left ambiguous, but Gaia's soul cycle appeared to have been freed as the Iifa Tree seems to have collapsed, and by the time Tantalus Theater Troupe returns to Alexandria to perform I Want to Be Your Canary for Queen Garnet, Mist had disappeared from the world.
- Kuja talked about the "souls" in plural, so he may have gotten such a sustained Trance by taking many souls and having them all enter Trance simultaneously.
- Final Fantasy IX, Kuja: "I just needed to borrow the power from wretched souls that can't die... Where did I acquire it? It was the Invincible, or should I say, that large eyeball in the sky? The ship sucked up the souls of Madain Sari, the Iifa Tree, Alexandria, to feed upon them..."
- Final Fantasy IX, Soulcage: "Mist is a by-product of the refining process. It is discharged through the roots."
- Final Fantasy IX, Garland: "I constructed the Genomes to be vessels for the souls of the people of Terra when they awaken."
- Final Fantasy IX, Zidane: "I'm alive! I have a soul! Why is everyone here so..."
Girl: "Because you are...special. [...] We are mere vessels. You have been given a greater purpose."
- Final Fantasy IX, Vivi: "Farewell. My memories will be part of the sky..."
- Final Fantasy IX, Voice: "The body becomes a vessel, which greets a new soul..."
Garland: "He's too good to make into a regular Genome... But I have no choice."
- Final Fantasy IX, Mikoto: "We want your memory to live on forever... ...to remind us that we were not created for the wrong reason–that our life has meaning."
- Final Fantasy IX, Kuja: "I must destroy him before Terra's plan is activated, or my soul will no longer be my own!"
- Final Fantasy IX Ultimania p.042
- Final Fantasy IX, Kuja: "That means...I simply need a powerful soul, even if that soul is not my own!"