Vanille and Fang were responsible for Dajh's fate
Before they're nabbed by PSICOM, Sazh reunites with his son, Dajh, and watches in horror as his flesh and blood becomes a crystal after having apparently completed his Focus of bringing Sazh and Vanille together. As if this weren't heart-wrenching enough, PSICOM leader Jihl Nabaat reveals to Sazh that Vanille and her friend Fang (yes, the same one chatting it up with Snow) are ex-l'Cie warriors who's presense at the Euride Gorge energy plant during a visit by Sazh and Dajh triggered the fal'Cie Kujata to awaken and turn Dajh into a l'Cie. Shockingly, Sazh does not take the news lightly and Jihl sets him loose to exact revenge on Vanille. Ever the moral man, Sazh stops himself from killing Vanille, and after a brief fight with his Eidelon, Brynhildr, they wind up on the PSICOM ship Palamecia with a one way ticket to execution.
Time Out: Eido-what?
Hold up ... Eidolon? What's an Eidolon (we imagine you asking)? By this point in Final Fantasy XIII, a couple of characters have already gone toe to toe with these massive creatures, which can be summoned forth in battle for assistance once they are initially beaten in the wild. In short, Eidolons are the goddess Etro's real world ambassadors who live in crystals called Eidoliths. Eidolons appear to l'Cie who need them most; which in this case, is everyone in Lightning's crew.
And now back to the plot...
The head of Sanctum was a fal'Cie all along
Dun, dun, duh. In a stunning, there's-no-way-you-could-have-guessed-it twist, the head of Sanctum, Primarch Galenth Dysley, is revealed to be the Cocoon fal'Cie ruler Barthandelus and one of the game's main villains. He is the one responsible for moving the Pulse Vestige into Bodum in the first place, setting Serah, Lightning, and Snow along their paths. As bad guys are wont to do before beatdowns, Barthandelus delays his ass-kicking to tell Lightning and company that their Focus isn't to save Cocoon, but rather transform into the beast Ragnarok and destroy it by killing the fal'Cie Orphan. Remember when we said being a l'Cie wasn't a picnic? This is why.
The fal'Cie wanted to resurrect their Maker
The gang escapes Barthandelus with more than a few scratches, only to have their minds blown by Cid who explains the whole goal of the fal'Cie Barthandelus included is to kill the fal'Cie Orphan who is keeping Cocoon aloft, thus sacrificing millions of humans to resurrect their Maker. They need l'Cie to carry out this gruesome act, as fal'Cie are bound by Square Enix logic to not kill themselves or each other. Sure, they can create a whole civilization and manipulate them into killing each other, but going about it directly is a big fal'Cie no-no.
As for who this Maker is, that's open for interpretation. Depending on which fal'Cie you ask (and assuming you can even book an interview), it could be Pulse, Lindzei, Bhunivelze, or another god we don't know about yet. Nevertheless, the fal'Cie aim to meet their Maker by overloading the door to Valhalla Etro's Gates -- with millions upon millions of human souls.
Vanille and Fang almost destroyed Cocoon, but failed
That's right: The Vanille you've likely come to love and/or mute almost annihilated humanity. She confesses this fact aboard Cid's ship, telling the gang that she and Fang were once l'Cie charged with turning into the monster Ragnarok and destroying Cocoon some five hundred years ago during an event called the War of Transgression. Thankfully, they were not successful. In the end, Fang alone transformed into Ragnarok but only managed to take a dent out of Cocoon. The kicker? Fang and Vanille's fal'Cie was none other than Anima, and their resurrection from crystal status in the Pulse Vestige is what kicked off Bodum's Purge.
Etro saved Cocoon the first time
Remember Etro? One of the original gods Bhunivelze banished to Valhalla for looking like her mom, Mwynn? As it so happens, not only does humanity owe her for their existence, but Etro was also the being who turned Fang and Vanille into crystals before they could bring Cocoon crashing down. In so doing, this ended the War of Transgression in which Pulse citizens attempted to invade Cocoon, thus continuing an ages-old feud influenced by fal'Cie on both sides.
Orphan merged with Barthandelus
With the fal'Cie's plans laid bare, the gang vows to save Cocoon from its fate, even if it means rejecting their Focus and turning into Ci'eth. After some meandering on the surface of Pulse and trying to wash off their l'Cie tattoos in the town of Oerba (the former home of both Fang and Vanille) they encounter Barthandelus once more and discover he is manipulating the Calvary to attack Orphan, with hopes of killing the Cocoon fal'Cie and doing what Lightning and her team refuse to do. After another rousing battle, the gang rushes to Cocoon's capitol of Eden, home to Orphan's Cradle, only to find Barthandelus and Orphan have become one. Seeing no other option but to fight, Lightning and her friends engage the hybrid villain in a final showdown with earth shattering results.
Fang almost destroyed Cocoon ... again
During the end-game face-off with Orphan-Barthandelus (Orphbart? Barphan?), Fang is forced to transform into Ragnarok once again and land the finishing blow on Orphan. The other members of party (briefly rendered Ci'eth) get their human acts together n time to stop Fang from transforming and together they beat Orphan for good.
Wait, you say, wasn't the whole point to keep Orphan alive? Wasn't it Orphan's plan all along to die by the hand of l'Cie, thereby setting off Cocoon's destruction and the return of the "Maker". Why yes. Yes it was.
Fang and Vanille saved Cocoon (for a change)
With Orphan out of the picture, Cocoon falls like a rock and everyone but Fang and Vanille turn into crystal as a reward for bringing humanity back from the brink of annihilation. Determined to save their friends, the ladies give into their Ragnarok urges and transform into the legendary beast. This time, however, it's a good thing, as the transformation allows them to crystallize into a colossal pillar which catches Cocoon and prevents the artificial planet from crashing into the surface of Gran Pulse. Hurray!
Wait...but what about...
Don't worry, Etro cut everyone a break
According to the rules, Lightning, Snow, Sazh, Serah, and Dajh should have all ended the game as life-sized statues. But as we know, Etro doesn't play by the rules. So, as a nice little gift for restoring balance to the world and not allowing the Etro Gates to burst open, the goddess frees the gang from their crystal prisons and erases their l'Cie tattoos. Friends rejoice, families are reunited, and somewhere a fal'Cie gets its wings...or something. All's well that ends well, right? Wrong.
