Gran Pulse and Cocoon
Thirteen centuries ago, humans lived on the world of Gran Pulse, a huge, wild, untamed planet. The fal'Cie didn't care about them, and merely cultivated the land, sometimes making or changing creatures, but never really directly affecting human affairs. Nature was savage and unkind, and humanity struggled to survive, having to fight for its right to exist. Then one day kind Lindzei, filled with sorrow and compassion for mankind, created a utopia in the sky: Cocoon, the shell planet. He invited the people of the world into his paradise, and they were tempted.
Cunning, scheming Pulse, however, had different plans. He spread lies and corrupted the hearts of men, and jealously kept some of them even as Lindzei brought more and more people to his paradise. They reached a stalemate, but it was unstable. The people of Gran Pulse were envious of their siblings on Cocoon, and sought to destroy them and bring them down, while Pulse whispered his evil words into their ears. The conflict escalated, with battles between the two worlds growing more numerous and frequent, until one day seven hundred years later Pulse picked two girls - the chosen ones - to bring down Cocoon once and for all. They were l'Cie, and together they would become the giant beast Ragnarok, and tear that perfect little moon from the sky.
But something happened. Ragnarok was incomplete - one of the girls couldn't become it - and all it could do was crack the planet's surface, in what would become known as the War of Transgression. Cocoon turned the tide of battle, and the horrendous beast disappeared. Humanity was all but wiped out from Gran Pulse, and while Cocoon's citizens suffered for them, death was surely better than Pulse's corruption and the hellscape that was the world below. The Cocoon fal'Cie have ever since been restoring the damage caused in the war, getting raw materials from savage Gran Pulse to rebuild. Lindzei and Pulse departed, never to be seen again.
Cocoon has known six hundred years of bliss and peace. They will soon end.

Magic, the fal'Cie, and l'Cie
The fal'Cie (fahl-see), our gods, walk amongst us.
They don't really walk. They are god-machines, grown around the magical crystals in their cores, built for specific tasks and singleminded in their desire to fulfill them. Pulse is one of them, as is Lindzei. The fal'Cie of Cocoon make sure it remains a paradise, giving people their food and basic necessities and entertainment. They rule and run the entire planet, from water treatment to electricity, making sure the cities all work and no one needs for anything. When Cocoon needs something it doesn't have, they reach for the necessary materials on Gran Pulse and fetch them, fashioning them into whatever it is. There are fal'Cie on Gran Pulse, too. They make sure natural selection keeps working, like Titan, or perform duties none understand, like Atomos. They are largely indifferent to humanity, and go about doing their unfathomable duties all the time.
When fal'Cie need a task done that they cannot do themselves - for they have no free will, and cannot deviate from their plan - they pick humans and choose them for a task, a Focus. These humans are l'Cie (luh-see), chosen of the gods, and are marked with a Brand (that has a magic crystal called Eidolith hidden in it) and given a vision of the task they must fulfil. l'Cie can use magic, unlike normal humans who must rely on magitek with mana extracted from crystals to do it, and become stronger, faster, more resistant, and overall better, all with the intent of completing their Focus. Once a l'Cie's Focus has been completed, they enter Crystal Stasis, becoming immortal and spending the rest of forever dreaming. If a l'Cie takes too long to complete it, fails, or gives into despair, they become Cie'th (seeth), twisted monsters of negative energy, forced to relive their failure forever, until someone completes their Focus for them or slays them. After long enough, a Cie'th loses all of its will and mind, becoming a Cie'th Stone. In this state it's no longer a threat, and only floats there, calling out to nearby l'Cie, begging for someone else to complete their Focus so they can finally rest in peace.
Magic powers typically comes in six "packages" or "roles." You can only have one active role at a time and do magic associated with it, but switching roles is an instant, costless action. The roles are Commando, Ravager, Sentinel, Saboteur, Synergist, and Medic:
- Commando does physical enhancements and boosts to oneself, and has strength-related magic that takes a while to dissipate. When in the Commando role, you can chain magic and make it more robust to time and dispelling;
- Ravager does magical enhancements and boosts to oneself, focusing on combined magical effects and stuff involving the elements. Ravager magic builds on magic that's already there but is unstable, dissipating quickly;
- Sentinel does defensive magic, physical and magical resistance, both on oneself and other things and people;
- Saboteur does magic that debilitates things and people, like poisoning or weakening or slowing down;
- Synergist does magic that boosts things and people, like strengthening or speeding up or giving cognitive enhancements;
- Medic heals and repairs its targets.
If a l'Cie finds themself faltering in their Focus and losing hope, falling prey to despair, they get one chance to change their minds, a challenge sent from the gods. This challenge comes in the form of an Eidolon: a mechanical creature that emerges from the l'Cie's Eidolith and challenges them to combat, questioning their will to live. Once defeated, an Eidolon can be called by the l'Cie at will, to stand with them in combat or help them in various other ways. Eidolons typically have two forms: one "humanoid" and one that's more of a "vehicle" of sorts, like a car or a horse or a dragon.
The Pulse l'Cie
Inside a tower that was brought to the city of Bodhum from Gran Pulse, a fal'Cie was found. Fearing that anyone in the city at the time of its discovery might've been infected by it, Cocoon's governing theocracy, the Sanctum, enacts a Purge: the city's quarantined, and everyone in it is to be sent to Gran Pulse, known to Cocoon citizens merely as Pulse. And their fears were not unfounded: one girl, named Serah Farron, did in fact enter the Pulse vestige and was branded a l'Cie by the fal'Cie within, Anima. Serah's sister, "Lightning" Farron, a member of the military department of the Sanctum, the Guardian Corps, sets out to save her, volunteering for the Purge so she can go into the Pulse vestige and rescue her. She ends up having to ally with Snow Villiers, Serah's fiancé (whom she does not like), a boy and a girl caught in the Purge named Hope and Vanille, and an airship pilot named Sazh, whose son became a Cocoon l'Cie.
The Purge was a lie; the Sanctum never intended to send all those citizens to Pulse, and merely wanted to kill them all. NORA, a group of neighbourhood watcher kids with Snow as their leader, serves as a resistance movement, trying to survive and escape the Sanctum's clutches. Hope's mother volunteers to fight, but dies before his eyes, and Hope blames Snow for this. As he tries going after the man and is trailed by Vanille, they all reach Serah, passed out in front of Anima, and as she turns to living crystal before their eyes, she tells Lightning to save Cocoon. Lightning attacks Anima, who brands them all l'Cie, and they receive a vision of the giant monster Ragnarok destroying Cocoon once and for all.
Snow vows to protect Serah's crystal while Lightning and Hope set out on a path of revenge against the Sanctum and the fal'Cie and Vanille and Sazh decide to run from their fate. They eventually run into Fang, a friend of Vanille's, who's working with a paramilitary group that wants to free Cocoon from the fal'Cie's clutches. The party finds out that the both of them are actually from Pulse, and are the girls who became Ragnarok and failed to destroy the world six hundred years ago. The girls explain that what they've been told is that Cocoon was a nest of vipers, created by fell Lindzei to lay waste to Gran Pulse and kill all they held dear. Their mission, to become Ragnarok and destroy Cocoon, was one of self-defence. It failed, for some reason, and they fell to crystal stasis before they could actually complete their goal. Now, having met Cocoon citizens and seen their god's words as lies, they want to protect Cocoon and not let it be destroyed. Dajh's son turns to Crystal at one point amidst this, his Focus having been to bring the l'Cie to the Sanctum.
Eventually, as the party runs from their pursuers, they're transported by the fal'Cie to the ruins of an Ark, an ancient technological structure meant to serve as training grounds for l'Cie that they become able to complete their Focus. After going through this, the party faces Galenth Dysley, the Pope figure that leads the Sanctum. He reveals himself as Barthandelus, the fal'Cie who leads all of Cocoon's fal'Cie, and explains that he is actually behind all of this: the party's purpose is to destroy Cocoon so that when all the souls of the people living in it go through Etro's gate, it opens wide enough that the fal'Cie can go through. He says that they've been looking for their Maker since always, tasked by Lindzei and Pulse to do it, and that opening the gate of the dead will allow them to finally reunite.
The Truth
A long time ago, Mwynn created the world, which was divided in two: the mortal world, realm of the living, and the unseen realm, the realm of the dead. She had a son, Bhunivelze, who was jealous of her power and understanding of the Mortal World, and who believed she had cursed the mortal world to eventually be destroyed. He sought to kill his mother once and for all, but if he went into the unseen realm he would lose control over the the mortal world. He created the fal'Cie Pulse, to scour the world in search of the gate of the dead, and then created the fal'Cie Etro, to assist him. Unknowingly having made her in the image of his mother, however, he never gave Etro any powers and discarded her, creating Lindzei instead. He fell into a deep crystal sleep, to wait for the day when Pulse and Lindzei found the gate.
Etro became depressed by her lack of powers and purpose and killed herself, vanishing from the mortal world. From her blood, Lindzei created humanity, setting it on Gran Pulse to thrive. Meanwhile, Etro found Mwynn being consumed by chaos, and with her dying breath Mwynn tasked Etro with protecting the balance of the universe, for if the balance of reincarnation between the realms was broken the whole world would be destroyed; Bhunivelze had caused the curse he'd tried to prevent. Not fully understanding Mwynn's request, Etro took a shining to the humans who would all join her in the unseen realm, and started placing a piece of chaos in them as they left the unseen realm to be reborn in the living world. This piece would be called the heart, and it is the source of their emotions and free will.
This chaos was the stabilising influence the world needed, and the cycle of reincarnation kept the world stable. As Pulse and Lindzei continued to search and protect, respectively, humanity flourished, and after Cocoon was created, the two gods left the world, and Etro became known as goddess of time and death.
The Fall of Cocoon
After temporarily defeating Barthandelus, the group travels to Gran Pulse to try to search for hidden truths and figure out what's really going on. Finding that all that's left of humanity on Gran Pulse are ruins, they gather this information and become stronger. They visit Fang and Vanille's old village, Oerba, whence the fal'Cie Anima came, and Barthandelus confronts them again, saying they can't flee their fate. He gives them an airship to return to Cocoon once they're ready to embrace their Focus and destroy the world, and leaves.
They decide they will confront Orphan, the fal'Cie who powers all the other fal'Cie on Cocoon, and try to fight Barthandelus and break free of their Focus. Once they reach Cocoon - in a state of chaos, for the Purge was illegally televised and now people are aware of the Sanctum's corruption - they fight their way to the heart of the planet, where the fal'Cie Eden, that keeps it afloats, sleeps with Orphan. They discover that all fal'Cie are in on it, and conclude that there is no way for humanity to coexist with them peacefully, if the fal'Cie see them as mere pawns in search of their maker.
They fight and defeat Barthandelus, Orphan, and Eden one last time, but this causes Cocoon to lose its support and come crashing down on Gran Pulse. Fang and Vanille, taking their Focus into their own hands, join into Ragnarok, but instead of destroying the world, they create a crystal pillar that holds it aloft, allowing the people to descend from it and settle on Gran Pulse, free from the fal'Cie's grasp. Having arguably completed their Focus, the party turns to crystal, but the goddess Etro takes pity in them and releases them - with the exception of Fang and Vanille - from their stasis.