After it is revealed Noctis is the Nothing and actually the supreme being of the FNC universe all along (and in fact he created everything to use as a training exercise for himself, so he can one day become strong enough to break free from the universe to devour other universes).
Vanille (turns out she was a *Flawless l'Cie from Novus from 20,000 years ago) absorbs the power of Chaos by using her brand on her left iris (that was hidden... which contrasts with Noctis brand on his right eye!).
*Long story short but <insert background info that explains what Flawless l'Cie are and how they can absorb Chaos and how they are awesome and can only be branded by being awesome like Vanille is awesome>. Also Vanille was totally part of the Nine from Novus created to fight the Nothing.
(Disclaimer - I changed some things from the Versus XIII link. The Flawless were just regular crystals that simply weren't corrupted by the Nothing yet. I changed it to make Vanille overpowered because I love Vanille, so therefore she is overpowered.)
Anyway the two fight but Noctis/the Nothing keeps coming back (it can't truly be defeated).
So Vanille does the only thing possible - She combines with Noctis / the Nothing (sort of similar to Vanille + Fang into Ragnarok but they stay in human form for coolness factor) and "
they.... become one!".
Que something similar to
trailer for Wrath of the Lich King where Vanille's friend (with Vanille originally being from Novus) goes:
Cocoa (see what I did there?): My friend... the day you were branded... the very forests of Novus whispered the name "Vanille". (Obviously because Vanille is that awesome.)
Que epic cutscene where Vanille/Noctis finds an icy planet to sit on a throne (to mimic the WotL trailer) then gets back up to display their epic powers.
Cocoa: And I know you will show restraint when exercising your great power (Vanille).
Vanille then busts out her Scythe (ATB Skill Death = Scythe fits right?) and uses it to break the ice then they summon corrupted fal'Cie (which includes Titan and Bhunivelze) with their power (now controlled by Vanille/Noctis). Also a big explosion occurs because irony needs to happen.
Then they break free from the universe to devour other universes (not Vanille but Noctis leading them). To be continued.... in FINAL FANTASY XIV!!!!! Oh noes! Evil plan by SE to make people get FFXIV! (Same strategy by Blizzard except more epic and actually planned from the very beginning!)
Also there are totally several hints that show that Vanille is really the counterpart to Noctis:
1. Vanille is outgoing and active, while Noctis is reserved and shy (according to SE).
2. Vanille dislikes having to hurt and she tries to avoid it as much as possible, while Noctis doesn't care. Also Vanille wants to save worlds, while Noctis wants to devour worlds.
3. Vanille is hotter, while Noctis is much less hotter. Both Fang (and totally Lightning too, both from Gran Pulse) and Cocoa (friend from Novus) want Vanille, while we don't know of anyone that wants Noctis (so Vanille is clearly objectively hotter than Noctis).
THEY WERE CONNECTED ALL ALONG GUYS!!! See how they are counterparts to each other? Truly Noctis required Vanille to be complete.
True story.... Of course that (Vanille + Noctis combining) really ends up being one of the 4 "what if" endings you can get in Versus XIII when you play Vanille's part where Cocoa (her friend) sends Vanille from Novus to Gran Pulse (and gets inserted with fake memories then becomes "Oerba Dia Vanille" from Etro). You play out the part where Fang turns into Ragnarok then you have 4 choices - Let Cocoon fall; absorb Chaos (which branches into two more options: Escape from the Nothing by breaking free from universe using the absorbed power of Chaos or fight the Nothing and combine with it to become one!), fight Fang/Ragnarok using Novus l'Cie powers (but magic aggro the Nothing, who is on Novus, and risk the end of everything as we know it), and finally of course call out to Etro to crystallize her and Fang (what actually happens).
So the ending where Vanille + Noctis combine (and mimic the WotLK trailer) is actually a "what if" ending in Versus XIII.
Really what happens at the end of XIII-2 is that all the Chaos released is absorbed by Vanille's Novus l'Cie brand. She breaks free from her crystallization, then breaks the Divide (which undo Lightning's turning into stone and Serah dying, syncs the timeline with FNC, and also leaves Caius crying with Yeul being disappointed at him), then breaks free from the universe and is lead to the universe of FFXV by her brand.
At the end of FF Versus XIII (which happens later after XIII-2) - Noctis finally becomes strong enough to break free from the universe and heads for the universe of FFXV too.
Vanille and Noctis fights in an epic battle to determine not the fate of one universe but the fate of all them!!!!!!!11 (Also the universe of FFXV is the same universe Vana'Diel is in!!!!)
(With FFXV being a single player FFXI of course.) Well either that or they head to the universe of FFXIV and Noctis becomes a boss in an expansion pack but no one wants that right" (inb4 SE copied Blizzard)
(Also the Nothing has a big magic aggro that detects Vanille's Novus Flawless l'Cie powers hence why she never uses them in FFXIII+. Etro sealed her memories of her past on Novus and inserted fake ones.)
(Also Gran Pulse is really inside the "Divide" which is sort of a semi-universe on its own with its fake artificial timeline that was created by Etro and powered by the Moon Cryst with the latter being powered by the Nothing which was all a plan all along to strengthen everyone, so it can fight them, so it can one day break free from the universe, so that it can setup the storyline for FFXV or appear in an expansion pack for FFXIV.
True story.)