Some of you may have read my "theory" about the end of chapter 2 in some of my previous posts; I'm creating this thread to get other people's perspective, thoughts, and/or theories of their own. This post covers the whole span of the game so if you haven't beaten the game DO NOT continue, unless you ok with having some of the story spoiled.

The matter in hand is whether Anima or something else branded Lightning, Snow, Hope, & Sazh as L'Cie. I'm on the record for saying that it is something else, exactly what I am unsure, though I have a theory, since the game doesn't offer that much clarity. After the fight with Anima the party is transported to someplace where a big crystal is floating in space. A gargantuan entity emerges from below, sends out energy tentacles, then proceeds to brand them as L'Cie.

The entity that emerges looks different from the "Anima" faced as a boss just prior and the only Fal'Cie we know that can change its appearance is Barthandelus for he is a Fal'Cie of illusion. Therefore without any evidence to say that all or a few (which would have to include Anima) Fal'Cie can change their appearance I take it as Anima and the entity being two different beings. There is also no evidence to suggest that "the entity" was Anima's true form.

My theory is that the entity was the god, Gran Pulse; I couldn't imagine the goddess Etro looking like that as "the entity" looked masculine, though she would be my second option. It could have been Lindzei though since Lindzei is mentioned to be a female as well, to me, the look wouldn't fit as well. As for the "dream" the party is shown as what their focus is could be interpreted in two ways depending on which god - if it was a god - it was that branded them. I've also stated before that the brief scenes that are shown in the "dream" are snippets of what happens in the end, however, their briefness does a good job of making the party - and the player - to believe that Lightning and company are supposed to destroy Cocoon. Since the "dream" is small bits of the ending it could lead to that the party was supposed to save Cocoon. That theory would be in line with Gran Pulse and Etro who are the "good" and "neutral" gods in the pantheon, Lindzei being "evil".

Another way to interpret it is that the "dream", as is its nature, is vague and the specifics (such as destroying or saving Cocoon) are not set in stone; this would fit if it was Lindzei who branded them. Though why Lindzei would want to destroy Cocoon wouldn't add up. Lindzei crafted Cocoon as a "paradise" for men and those who left Pulse for Cocoon were seen as slaves of the Demon Lindzei by their Pulsian counter-parts (Analect II. Lindzei's Nest). It was Barthandelus and the other Fal'Cie of Cocoon, whom were Lindzei's brood (Analect VIII. Fell Lindzei), who wanted to destroy Cocoon so that they could find their maker; or so they could fight the "menace" from "beyond"; the gods were theorized to residents of the "beyond" ((Analect X. The Menace Beyond) which is another matter if the Fal'Cie wanted to challenge the gods). However there is one Analect saying that Lindzei wanting Cocoon destroyed - Analect IV. The Heavenly Deceit:

Ragnarok took wing; made to smite Cocoon, and thereby deliver us our everlasting peace. But Her Providence would not let it be. The Goddess pitied the fools who so blindly bowed to Lindzei's will, and so She robbed Ragnarok of power, putting the l'Cie to an early crystal sleep, Focus yet incomplete.

This would suggest that she was able to manipulate the Pulsian Fal'Cie, whom are children of Gran Pulse, into doing her will. As to why she would want Cocoon destroyed, I theorize, is not for the same reason why the Cocoon Fal'Cie wanted it destroyed. In the Analects it is said that the Maker, presumably Gran Pulse, forged Man from traces once Divine (Analect I. The Vanished Gods); Lindzei is only credited with creating her own Fal'Cie (Analect VIII. Fell Lindzei), since she was the "evil" goddess in the pantheon her intention of destroying Cocoon would be to destroy a creation of Gran Pulse's - Man.

As to support my theory there are two datalog entries , the final two for Chapter 2: Pulsian Menace & Bound in Darkness. In the "Pulsian Menace" entry it states: They work together to bring down the fal’Cie, and the Vestige now plummets towards the lake below. A final wave of power explodes from the dying fal’Cie, transforming the water and surrounding into solid crystal. Lightning and the others do not witness this breathtaking event -- upon
defeating the fal’Cie, they are drawn through a rift into a dimension where an
immense, otherworldly presence awaits. Onto their bodies, it sears cursed brands; onto their minds, the vision of a beast destroying Cocoon. Swept along by unimaginable energies, the helpless companions are swallowed in a lightless void.

As it says the party is drawn through a rift into a dimension where an immense, otherworldly presence awaits. As it is said in the Analects, the gods left the world and are theorized to be residents of the "beyond"; the Cocoon Fal'Cie want to sacrifice Cocoon so they may open the doors to the "Divine beyond", since it is theorized that when a person dies their soul uses the same Door as the departed Gods used to reach the place that lies beyond (Analect XII. The Door of Souls). Since they were drawn to another dimension the only beings who are capable of that feat would be the gods; coupled with the presence waiting for them was "otherworldly" it could concluded that it wasn't a Fal'Cie since the party is accustomed to Fal'Cie.

The "Bound in Darkness" entry words what happened a bit differently but the message is the same: As they deal the killing blow to the master of the Vestige, a flash of light rends the air. They are pulled into a swirling void of chaos, where they are bound by an ominous and inexorable entity. Branded with arcane markings, the companions are then assaulted with the vision of a terrible beast tearing Cocoon apart. Soon after, the Vestige finally succumbs to the combined attacks of the Sanctum forces.

Here it says that they were "pulled into a swirling void of chaos, where they are bound by an ominous and inexorable entity". It isn't divulged in the game that Fal'Cie could use a "flash of light to rend the air that leads to a swirling void of chaos"; once again, the only entities capable of such power would be the gods since they are made of the "Divine" and are a higher being than Man, are able to cross at their liesure. Both datalog entries omit that it definitely was the Fal'Cie Anima who branded the party; if Vanille was originally branded by Anima 500 years ago she could have said Anima's name, softly so nobody would hear, in remembrance of old memories. Yet she says nothing and with the entity being otherworldly and that the party was drawn through a rift into a dimension that was a void of chaos it appears, to me, that it wasn't Anima whom branded the party.