Final Fantasy XIII-2 is a tale of multiple timelines
Proving that even gods can't mess with the rules, Etro's interference at the end of Final Fantasy XIII causes the timeline to become unhinged. It also results in Lightning falling between the cracks to wind up in Valhalla as the guardian to Etro herself, who is worse for wear after stepping in to save Lightning's friends. Final Fantasy XIII-2 picks up three years after the first game in a reality where Lightning has been yoinked from the timeline, leaving her team to believe she is stuck inside the crystal pillar with Fang and Vanille. All except for one...
Serah and Noel are the stars of FFXIII-2
Plagued by visions of a sister she knows is still alive, Final Fantasy XIII-2 finds Serah taking up the role of hero and setting off on a journey to rescue Lightning from wherever she disappeared too. Early into Serah's quest, she is saved by an amnesiac warrior from the future named Noel Kriss who acts as her companion through time. Noel knows a few things about Lightning, having fought with her briefly while passing through Valhalla before being spit up in Bodum. Together, they band to find Lightning and save Noel's future by mending paradoxes via the Historia Crux, a passageway through the time continuum.
Oh, and there's also Mog (kupo)
Don't forget about Mog, kupo! Mog is important too, kupo! Mog hails from the Ocean of Time, but was sucked into a paradox, and wound up becoming a weapon called Starseeker for Lightning in Valhalla, kupo! When Noel passed through Valhalla, Lightning gave him Mog to pass on to Serah, kupo! If you think this is annoying now, just wait, kupo!
Noel had his own reasons for helping Serah
Throughout their time travels, Noel comes to remember he is from a post-apocalyptic future where Cocoon has broke free of its Crystal pillar and crashed into earth. We also learn he hails from a tribe of Gran Pulse survivors called the Farseers who's population is in the single digits. Desperate to gain the power to change his destiny, Noel begged Etro to lend him a hand, and the goddess responded by opening a time gate to Valhalla and letting him slip through.
Serah was a Seer (and so is Yeul)
In the Fabula Nova Crystallis universe, there exists females who can see into the future and accurately predict the events to come. This ability comes at a grave cost, however, as Seers have a tendency to be driven mad and die from the effort it takes to receive said visions. In time, Serah comes to learn she herself is one such Seer, and she learns this from Yeul, one of Noel's fellow Farseer's from the future who is fated to die with every alteration the timeline, only to be resurrected again to meet the same fate.
Caius wanted to save Yeul by destroying reality
Caius Ballad is the chief bad guy in Final Fantasy XIII-2. In addition to being Noel's former mentor, he is a warrior who was given the Heart of Chaos by Etro, after which he became immortal and spent the rest of his days protecting the timeline and every version of Yeul throughout history. Like Barthandelus, Caius' mission is to open the gates of Etro and destroy the very fabric of reality. Unlike Barthandelus, his motivations are a little more noble (well, as noble as a mass murderer's motivations can be). As it turns out, Yeul's continual cycle of death and resurrection has driven Caius mad, and the only way he can think to end her suffering is to find a way to kill himself and erase the barriers between Valhalla and the real world. As it turns out, it is Caius who has been setting up the paradoxes, orchestrating events so that Noel would have no choice but to wind up in Valhalla and kill him.
Meanwhile, Hope builds a new Cocoon
While Serah, Noel, and Caius and busy shouting exposition at each other throughout the timeline, a grown up Hope gets busy building finding a way to save Cocoon from crashing in the future after learning of its fate from a vision left behind by Yeul. His first method, a Proto fal'Cie, fails miserably, nearly ending in everyone's demise. His second idea, a brand new Cocoon called Bhunivelze (pop quiz: where have you heard this name?), is more successful thanks to the installation of a few graviton cores found by Serah and Noel. We say a little because while Bhunivelze does make it off the ground, by the time the credits roll, it's future isn't looking so bright.
Caius was destroyed, and the world was saved
Serah and Noel eventually leap their way to Valhalla where they confront Caius' Jet Bahamut form. Determined to shatter his own Heart of Chaos for good, Caius goads Noel into striking the final blow. When Noel relents as he did years ago when he first met Caius Caius takes matters into his own hands and drives Noel's blade into his chest. Caius dies and the chaos inside of him is released. Noel and Serah make a haughty escape from Valhalla and arrive back in the real world to find Hope's Bhunivelze making its ascent.
...But not really
No sooner does everyone have a chance to high five atop Sazh's airship (oh yeah, Sazh is in this game too) does Serah have one final vision and die in Noel's arms. Things go downhill from here as an ailing Mog informs Noel that Etro is dead and everyone watches helplessly as the chaos of Valhalla slowly begins to seep into Gran Pulse and over newly launched Bhunivelze. Cue cliffhanger music.
The story continues in Lightning Returns: Final Fantasy
What happens to our plucky heroes? Is the world screwed for good? Does J-pop really exist in the future? All these answers and more will be answered in Lightning Returns: Final Fantasy XIII, a sequel which its developers promise will bring closure to Lightnings story. Read the latest details in Lightning Returns' bizarre details explained by Square Enix.