Zacharie is the guardian of Zone 0.
The Batter is a deity deciding that creation is corrupt and deciding to end it all.
It was Japhet's madness that made Dedan the jerk he is in-game.The room seems to imply the three were good friends at the start, and most of Dedan's cruelty is towards the Elsens. Perhaps seeing his friend try his best to please them, only for the Elsens to reject them due to their own paranoia, and watching him descend into madness due to his best efforts getting (unintentionally) thrown back on his face, embittered him against them. Perhaps he now thinks trying to be nice to the unappreciative morons that reduced one of his only friends to a violent madbird isn't something he's gonna do, and takes his rage out on his employees.
The game takes place within the Batter's mind as he achieves mental purity.He is freeing himself of all internal stress (Zone 1), worries (Zone 2), desires (Zone 3), and dependence (The Room).
When all of the zones have been purified, you can hear the Elsens' cries for help.When wandering the purified zones (1, 2, and 3), the piece heard in the background is called "Not Safe." The piece consists of whispering, desperate thumping and cries for help. During the game, Enoch mentions that without him, the citizens of the zone will fall into an eternal nothingness. It could be speculated that these cries for help are the Elsens lost in this nothingness and are desperate to escape, instead of them just disappearing.
The plot of the game is based around Batter's battle with and descent into possible schizophrenia.
Zacharie is OmnipotentThis is why he's one of the only characters you don't kill, one of the few that break the fourth wall, and the only one besides Batter and The Judge that's able to appear in Zone 0. It also explains how he's made out to be so important but outside of selling you goods and providing some exposition he really doesn't do much in game.
The "off" switch is for Hugo's life support machine.The entire game is a coma-dream of Hugo's, and represents his father trying to get through to him to tell him he has to die. He hides behind his childhood friends and his mother, and fears his father because he doesn't want to die, but in the end, the switch is still turned off.
Sugar killed everyone in Zone 0 beforehand.Knowing how sugar is made, it's somewhat suspicious how she manages to have so much in her room. Perhaps she was already mad and needed the sugar to calm herself, then had herself sealed in the basement by Zacharie after realizing what she just did.
The Judge is the Guardian of the "off" switch.And he has his title because he can judge whether or not the world continues to exist, which is why whether he lives or dies determines the ending. He was snapped out of his Despair Event Horizon by the Batter approaching the switch because he has a link to it, and he didn't oppose the Batter purifying other zones because there's a chance for things to be rebuilt as long as the switch remains "on" (chalk it up to the...unique morality of being both a cat and Guardian).
The Batter is a "failed" Guardian of sorts.Specifically, the "Death" to the Queen's "Life". The Queen is stated to have recreated the world, but may not have the capacity to destroy it, which is why she created the Spectres to correct things for her. Conversely, the Batter can only destroy things, which is why he spends the game purifying the world instead. In the battle against the Queen, she mentions asking the Batter to return to where he came from, possibly meaning another Zone, possibly the Nothingness.
Zacharie and Sucre are Hugo’s real parents.But they were separated from him when he was just a baby, so he made the Queen and The Batter to replace them. Now that Hugo is a small child, he doesn’t remember his real Mama and Papa, which is why he says in his diary/notes things that Zacharie is just his friend. Furthermore, Enoch is Sucre’s father, making him Hugo’s grandfather.
Hugo used psychic powers to revive his parents, and the Batter Came Back Wrong.After the End, exposure to fallout (it's been mentioned that the game's elements are all rumored to cause cancer, so nuclear involvement is likely) mutated his mother and father. Hugo was born sickly, but with powerful psychic abilities - as he was too young to control them, his mother channeled them to recreate the world. Of course, everything turned out more than a little strange as he knew nothing about the previous world or concepts like death, but the survivors figured it was better than nothing and set out to improve it. However, at some point, Hugo's parents succumbed to radiation sickness and died. Hugo brought them back, but in warped forms because of how he remembered them (the Queen's tentacles and "Bad Batter" were how they looked because of mutations). His relationship with his father further colored things; he's a sociopath because he neglected Hugo, who couldn't conceive of any positive traits in him. The final nail in the coffin was that the resurrection process seriously messed with the Batter's brain, which led him to try and wipe everything out and start anew.
The Batter's form changes depending on who's viewing him.This is confirmed with Sugar and the player alongside the Judge, but this could extend to other characters as well. Early on, the Judge mentions that the Batter has no "physical order", whatever that means. And while Japhet sees him as human, Dedan views him as one of the Spectres, and it's unknown what Enoch thinks of him. Perhaps only people who see the Batter as hostile can see his "bad" form.
Going off of the above, so does The Queen's.At one point, Dedan exclaims "By the queen's thousand faces!" despite the fact that The Queen hasn't a single face at all. Seems like just an expression, but we know that Dedan seems to respects the Queen a lot, and thus might view her as a powerful, eldritch being of some sort. Also, The Queen is somewhat presented as an opposite/equal to The Batter, what with having her own add-ons and such.
Going off of both of the above, The Queen is the sun that Enoch refers to.Enoch mentions that the guardians draw off of the infinite power of the sun, even though OFF does not appear to have a sun, nor a day or night in the first place. Recall that in The Room, Hugo's mom was represented in his drawing as a sun, and The Queen is supposed to replace his mom. Enoch has little respect for The Queen, since he immediately suspects you of being sent by her to stop him, so it's possible he views her as little more than an inanimate object, albeit a powerful one of which to draw his energy.
The secretaries are the lost souls of the elsens left in the zones when they are purified.The secretaries are described as demonic humanoid spirits. Maybe they're not really demonic but angry and seeking revenge on the batter for ending their lives?
The Batter is/was an Elsen himself.There are similarities between the Batter and an Elsen (one being appearance). It could be possible the Batter didn't want to comform to what the Elsen's way of life was (nothing but work). So, he donned a baseball cap, decided the Zone Guardians had to be destroyed, and became the Batter. The Batter doesn't make the noise that the Elsens do, because he doesn't want to have anything to do with them in that aspect. He keeps calm and collected (seemingly uncaring) in situations, so as not to get too stressed. What happens if you side with The Judge? He finally becomes stressed, and turns into the creature you see (his burnt form).
There is a power higher than the Puppeteer.During the beginning introduction it's said that "You have been assigned to a being called The Batter. The Batter has an important mission. Be sure that it's completed. We will let you out in Zone 0. Good luck." This implies that even though the Puppeteer is thought to be God, something is giving the orders.
If the Secretaries Divide By Zero attack was used anywhere else, it would cause a Reality Breaking Paradox......but in the Purified Zones, reality is already broken.
The Spectres are the angry souls of the Elsen.They are getting their revenge for being processed into sugar... And the Batter turning Elsens into Burnts and then slaying them sure isn't helping matters.
Zacharie will or has gone turbo before.
The Batter is performing the ultimate Mercy Killing.The Batter knows that the world he lives in is a Crapsack World, and wants to destroy it so nobody has to live there anymore.
The Batter is an adrenaline junkie.
The entire game of OFF is an alternate universe sequel to EarthboundAfter defeating the ultimate evil, Ness was extremely traumatized. His innocence was lost, and the boy's smile died with it. Ness grew up to be stoic, and chose to solemnly DESPISE everything corrupt on planet earth. He believed any and ALL evil in the world must be wiped out completely. Never again, did he want something as putrid as Giygas to pervade his home. In the event of a world shattering cataclysm, however, he vowed that he would take on the responsibility of being the world's savior and purifying the world with his PSI powers. Although Ness was perpetually solemn and viewed the majority of mortal existence as disgusting, there were a few things in life that made him genuinely happy. While his childhood friends eventually became nigh irreversibly distant, Paula was only a town away. She was one of the few things in his world that remained pure, the only friend who understood him. And of course, Ness never forgot his love of baseball. Paula and Ness followed one another into adulthood, and eventually got married. The day their little boy was born was supposed to be a happy one... ...Until the end of the world happened, via a nuclear fallout. A really, REALLY big one. Ness' world previously had its fair share of sentinent animals and creatures, but that was drastically reduced. And there were even fewer humans left. Most of those that were were mutated – including Ness and Paula. Paula had gained enough prestige as a psychic prophetess of sorts, and was unanimously selected by the remaining populous to be Queen. Likewise, Ness was widely respected as the Chosen One, and chosen to be king. After a couple years, Hugo grew more and more ill. Yet, he was showing signs of PSI/PK at an alarmingly early age. Ness was unable to aid, as he had lost much of his PSI/PK abilities in the mutation; Paula (now known as the Queen) managed to keep her powers, and even changed them a bit. Ness could never relearn PSI Heal, which is why he didn't revive any of the world's populous, or heal the remaining populous of their mutations and infirmities. He felt useless to the world, and to his family. The Queen did her best to care for her sickly child, and help him channel his powers through her own, but all they could do to keep him under control was imprison him. Ness, on the other hand, chose to depart for a few years, for various reasons. The idea of his only son being forced to live that way was unbearable to watch, he wanted to know if anyone else in the world had survived, and he wanted to find a way to fix the world. Maybe he could even regain his powers. Although much had happened, Ness still remembered his vow to help the world if a global catastrophe ever happened. After wandering for years in vain, he gets further and further out of touch with the last remnants of his humanity. No longer did Ness remember the love of his family – only that they existed. He felt little to nothing for them, as his mind couldn't supply the will to make such connections. Eventually, the world sinks into more hopeless ruin, and Ness is consumed by one idea: Purify the world... no matter the cost. Possibly in a last ditch effort by his subconscious to retain his humanity, he recalled a profound love for baseball. Ness rechristened himself as the Batter. Soon, he met up with the Judge. The sheer amount of concentrated will behind the Batter's ideology was so strong, that it was enough to make his powers return gradually. On his journey, he had been enlightened concerning some matters, such as the nature of Players and Puppeteers, and the role they played in controlling his world. So, he struck a deal with the Player/Puppeteer. By the power of hypnosis, mind control, manipulation of will — whatever you wish to call it – we agreed to help him with his unholy crusade. We had to know how it would all end, didn't we? Press start.
(Hey, you knew it was coming. Ness often uses baseball bats to attack, and regularly wears baseball caps. Paula seems respected enough in the Earthbound universe to be promoted to queenly status after a nuclear fallout wipes out the rest of humanity. It would explain why Hugo was born with psychic powers, anyway. Plus, Earthbound seems to know it's a video game, as evidenced by how it asks for the Player's name and asks the player for help in the final battle. Kind of makes a chilling amount of sense, when you think about it.)
The inevitable silly Alternate Character Interpretation
In the minor 'baseball game' metaphor, The Judge is the ball.The game begins with The Batter hitting The Judge with his bat, in the tutorial battle. At the end of the game, when The Batter has purified the zones/bases and returned to his home/home plate, he hits The Judge once again.
"Rubber" is actually an alloy of metal and plastic.Assuming that the world is made of only the four or five elements, that leaves some questions. For instance, we are told that the fences in the residential area of Zone 2 are made of "soft, harmless rubber", which is not mentioned in Zone 1 at all. So where does rubber come from, and why is it not an element? Perhaps because it is two (or more) elements. It can't be just one, because then it would be just that element, not rubber. Smoke is out of the question, because you can't really make something solid out of that. Meat wouldn't be too feasible either, because it probably has an expiry date. And sugar? No one would waste something so precious on things like fences. So the only things left to consider are metal and plastic. Which makes sense, considering metal is solid enough and plastic would be soft enough for a "soft, harmless" fence. Plastic + metal = fence, Q.E.D.