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A lot of people argue of the "true" meaning of Binding of Isaac, here's my take on the story, enjoy:
Before I get too philosophical, allow me to remind you this is all my opinion based on what I saw and so on. You might feel differently, and that's fine, just so long as you know this is what I think.
First off, let's look at the common themes in the game:
Possibly the biggest and most prominent theme, Binding of Isaac represents a story of betrayal from the point of view of a child. Psychologically speaking, Isaac is raised to accept his Mother and his god as being the two things in the world that will love and care for him unconditionally, as is typically the case with most children naturally. When Mom tries to kill Isaac, this presents a breach of trust. Even if you discount God as having instructed Isaac's Mom (leaning instead to beleive that it was Satan or her insanity), God never truly comes to save Isaac, so any hope of God saving his soul seems to go out the window.
Faith in the unknown
Isaac has been betrayed, that much is true, but once in the basement he is faced with a major decision: maintain his faith in God, or forego his faith in lieu of his own skills/abilities. Faith becomes a common theme at the end of every floor, where Isaac is forced to take a leap of faith into the literal unknown, delving into what will likely be the end of him. He could simply stay put and hide away in the shadows, but refuses to do so.
All throughout the Binding of Isaac, Isaac is forced to alter himself, giving up little bits of who he is or used to be in order to "build" himself to face Mom, even at the cost of his own body and soul. In essence, Isaac must stop being who he used to be and create a new, stronger persona to fight if you get what I'm going at. Each of Isaac's alter egoes represents a different image of himself; they are all Isaac, but in the same sense they are different parts of his mind. Maggy is the innocent one, beautiful (at least to Isaac) and a lover, not a fighter. Cain is the scavenger; fast, tricky, rougish, able to use his luck to his advantage and make due with what he gets (pills). Eve is Isaac's inner sadness, the dark, depressed corner of his mind that takes refuge in acknowledging that all he/she has left is a dead bird; everything Isaac cares for is dead. Judas is Isaac's inner rage; he is fragile and easily routed, but is unflinchingly powerful, building still on his power and rage until it spirals out of control and consume him; he even gouges his eyes out in literal "blind" rage. Lastly ???, who can be taken either as a joke character or, more seriously, one can argue that ??? represents Isaac having simply given up. He's taken to a fatalistic frame of mind; what will come will come and he is already dead anyways so what's the point? All the hearts in the game cannot help him as he is already a lost cause, or so he thinks.
Sin and self Corruption
Free of his Mom's grasp, Isaac is essentially free in his own world, albeit still fleeing (on the Lamb :P) he is not restricted in what he can do, from playing with Razors, taking pills from Mom's meds, bombs, gambling, and so on. Satan himself presents the ultimate example of this. Since Isaac is free from Mom, he is free to choose his own path, even if that involves making a deal with the devil himself.
So what does it all mean? In my opinion, Isaac's journey, at least from the moment he enters the basement, is likely all in his head. It presents a psychological battle of trust and self-sufficiency. Killing Mom and breaking her heart and, ultimately tearing himself from the Womb, represent the ultimate detachment from his Mother. He is acknowledging that he must break ties with her. Using the Bible, a metaphorical embodiment of Isaac's faith in God, Isaac instantly cements his faith and eradicates Mom who, with God at his side, cannot harm him.
In the same sense, Satan presents a similar mechanic. He is told he is "corrupt by sin" and delving straight from the Womb into his own soul, which he imagines as the Hell he is told of in myth and bible, where he must confront Satan within himself, killing him not literally, but metaphorically as he cleanses his mind. Using the Bible here doesn't make Isaac stronger, but immediately attacks his insecurity showing that his faith is ultimately not strong enough. After killing Satan and cleansing Sheol of evil, Isaac suddenly flashes between his alter egos and becomes aware of himself, ultimately realizing what he's done, what he's become, and locks himself away, perhaps either to keep himself safe from the brutality of the world, or to keep the world safe from himself. Basically, Isaac willingly "binds" himself, thus the Binding of Isaac.
Once Isaac has thoroughly cleansed his mind by taking the hopeless ??? to the deepest corners of his mind, he is rewarded with the two ultimate items: A D6, granting him ultimate control over his own mind, and the Forget-Me-Now, his ULTIMATE way of opposing Mom by doing the number one thing all parents forbid their children to do: taking drugs.
What comes next?
This section might get deleted as soon as WotL is actually release and speculation turns to fact, but I'm going to talk about what BoI is probably going to go:
At this point, finishing the game, as I've mentioned, results in Isaac slaying his inner demons and sealing himself away as either an act of self defense or an act of self-destruction, that being said, an opposite, true ending, would be very different. I feel the game will end with Isaac, as opposed to slaying his personal demons, instead accepting them possibly instead fighting a boss that, like It Lives, is a bodily representation of himself, who he will need to defeat. Surely "the Light" is a possibility, it certainly makes sense, but not in the "God is your next target or going to Heaven sense" rather in that Isaac is turning to the light side and accepting his imperfections, after which I beleive Isaac will either wake up from a nightmare or will find himself free from his mother back in the real world. Perhaps the player will be forced to cleanse themself in this new ending, stripping themselves of treasures or facing a boss that in some way reflects your player image ala Dople or Dark Link if you know what I mean. The final ending will, rather than representing the previous ending in which Isaac seals himself away, will represent a metaphorical freeing of Isaac, who will "unbind" himself, as opposed to binding himself willingly as before.
MORE COMING SOON: Item analysis, more character analysis (seperate and in depth), possible conclusion and more thought provoking stuff.