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The people aren't evil - they're trying to cure a plague.
Thinking about the parasitic worm you pull from the pig, perhaps it's not limited to pigs. Perhaps this is a natural plague of worms that has turned a number of infected organisms (people included) into mindless zombie-like entities.Perhaps the scientists are not the ones engineering the mind-control - perhaps they're actually trying to cure a pandemic of parasitic mind-controlling worms. Before it's too late...

The whole game is a Stable Time Loop
The Boy was created and is controled by (or IS) the dying Body of Bodies Blob Monster.
In the first "run" The Mermaid (a previous attempt to create a living relay for the Mind Control Facility) gifted The Boy with her powers (Being able to breathe underwater and a higher place in the Mind Control hierarchy) and he is then absorbed (Not without having destroyed all the Orbs Relays beforehand) by the Body of Bodies Blob Monster, giving it the ability to control the Drones without being mentally and physically constrained to a machine in its pod; It escape and dies.
In the second "run" The Boy unlocks the door of the secret vault and unplugs the Mind Control Facility, disabling himself, the Body of Bodies Blob Monster and all other Drones.
The Orbs Collectibles being reset after the second ending is a "proof" that playing a third (or more) time is non-canon and not a part of the story.
How can the Body of Bodies Blob Monster / The Boy travel back in time ? Maybe because of its sheer psychic power, the strange nature of the complex, the powers given by The Mermaid or some weird interaction between these three things.

The Boy is actually being controlled by a former employee
Remember the part where you had to roll through someone in order to progress and unambiguously kill him? What if this whole thing was a revenge plot by a former employee, who understood the Mind Control technology far better than anyone else in the company did? Notice how, at certain points in the game, some of the employees seem to actually be helping the blob-monster out, like opening a door and pulling the cord on the propelled platform-cubes. These might have actually been the protagonist's old friends, and somehow recognized them despite the horrific form they've taken.
  • This seems unlikely, as they were helping you get to the trap room, where you would have been stuck if you hadn't ripped the wall lining out to find a hidden grate.
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  • This is actually especially an unlikely theory because you have the option of not killing that CEO-esque person. If you wait a bit longer while he's scared and against the window he'll go to hide behind a plant and get out of your way.

All the controllable people are Homunculae and so are The Mermaid, The Boy and his Brother.

All of the people you control in the game aren't actually "human", in that they weren't born. They're artificial humans made by whatever companies the masked people are part of, constructed for menial labor and such. This is why all the ones we see without clothes including The Mermaid and the Boy(s) have no genitalia even when looked at right from the front. The technology is still very new, which is why they need such a goddamn huge facility to run it. Now, this process isn't without its detractors, but the people running the company are absolutely certain it's the way of the future, hence why they bring in their children. To get them acclimated to the horrors. This also explains why the homunculae become uglier the lower in the facility you get. Only the prettiest ones are allowed topside to be potentially seen by the public.


The Mermaid was an attempt at making sort of a superspecimen. One that was more durable, less uncanny valley-ish, and maybe even capable of running without human input while ordering around the other homunculae. This was a mistake, as The Mermaid became self aware and started acting out. This eventually resulted in her flooding a large part of the base, since she knew they couldn't find her underwater. That's not to say they haven't been trying, however, as evidenced by the fact that they have submersibles ready-made. This explains both why she attacked the submersible (she knew it was a human tool) and why she's afraid to come out of the water (she knows that's where the humans and their dogs have control.)

This is where the Blob Monster comes in. The homunculae's physical makeup is far more...malleable than that of humans, and the malleability increases when kept in water for a long time (hence why The Mermaid was able to upgrade herself.) Finding this out, the company decided to experiment with combining homunculae for increased physical strength and dexterity without increasing production costs or control resources. This was kept at the very bottom of the facility because, A: It was just a prototype and wasn't working yet, B: That's where their best scientists and their main resource pools were, and C: It was freaking horrifying and they didn't need any more bad publicity.

And then there's The Boy. The Boy is essentially what The Mermaid was supposed to be: a less creepy homunculus with extreme reactivity and hypersensitive control responses, allowing him to be controlled without moving like a zombie and while actually displaying the emotions and subtle movements of the human controlling him. The problem was that The Boy was made by someone (possibly an employee, current or former) who was both brilliant at homunculus construction and control, and sickened by what the company had become. Thus, they decided to use their ultimate creation, The Boy, to try and take down the company. They did this by sending out The Boy to destroy all of the beacons or, failing that, to break their main project (the Blob) and cause as much destruction and chaos as possible. The Boy succeeded at both.

But then what about the other ending? Well, there's a reason The Boy was "The Boy" and not "The Man". And it wasn't to try and disguise him from the masked guys. They could tell he was what they were looking for. Instead, The Boy was small because half of the resources that would have been used for him were instead used to make him a twin. The Brother is The Boy you play as in a playthrough after you've found all the beacons. The company is in chaos and can only put up a token resistance (mainly consisting of the same guards, whose shifts have been extended without warning) because of the chaos The Boy has caused. The masked people are focusing on the problems brought about by the Blob Monster escaping, so they haven't realized all their beacons are broken. As such, there's no reason to guard the very last one, kept isolated in some cornfield someplace. Because they figured there was only one Boy.

But the person controlling The Boy released control once the Blob had escaped, hence why it just sort of lays there at the end. They did this so they could take control of The Brother, who they sent into the cornfield to break the very last connection and beacon, destroying the Masks control over the homunculae.

This is the fourth time the Blob Monster has tried to escape

The Blob Monster was either created or captured by human scientists (or is the result of a disaster and is being studied), and it keeps trying to escape. This is the fourth escape - throughout the game, as you go through the other facilities, you'll see numbers on the walls and floors. The first section, as you go through with the submarine, there are 2s here and there, the sections with the Mermaid (before and after you're "upgraded") are labeled 3, and the final facility has 4s. The Blob Monster has escaped and destroyed 3 facilities already, but the scientists keep re-capturing it and building a new lab for studying/controlling it.


This is the fourth experiment
Going off of the above WMG with the numbers, experiment 1 was the farm with the parasites controlling the mindless pigs - one of the secret orbs is in a barn that is filled with pigs which are still alive but dormant, just like the pig you pull the parasite from. Experiment 2 was the Remote Bodies. Experiment 3 was the Mermaid, and when it went wrong, the entire facility flooded, and the the fourth experiment is the Body of Bodies / Blob Monster. Experiment 4, however, gained sentience and was able to control The Boy to combine the results of the first experiments (mind control and water breathing) in order to break it free.

This entire game is actually a metaphor for the Game Development Process.
Much like how the End of Evangelion movie was a metaphor for the process of developing an anime (and of Hideki Anno's conflict with his own fans,) Inside is a metaphor for the relationship between a Video Game Player and the Developers of said game. The Boy represents the Player, walking through a pre-planned scenario, overcoming obstacles that were placed there for him by the Developers. There's evidence, looking at the game world, that the entire thing could be taking place inside a single facility. The numbered signs we see and the strategic placement of lights, shadows, traps and puzzles would hint that the entire world is an obstacle course and the purpose of the Boy is to make his way through it. The periods of the story when the Boy controls other beings is actually a metaphor for the Player's ability to control in-game avatars. These avatars have no minds of their own, they're just extensions of the will of the Player. To further the "Boy as Player" metaphor, said Boy just pops into the story with no origin story and no introduction. This is because his purpose (while in the game world,) is to journey through it and stop once he gets to the end. The employees and Directors for the Facility at the end of the game are a metaphor for the Game Developers. They're the ones who've placed all of the obstacles in the game and are attempting to "kill" the Boy or prevent his progress. All through the game you can see the Facility People monitoring areas of the game. In the scene where the Boy has to pretend to be a Brainwashed slave as he parades before Facility Staff, this could be a metaphor for the act of Playtesting - the Developers are testing their scenario to see if the Players who enter it will "play" the way they want to. Any attempt to circumvent this by the Player/Boy will result in his Death/Stoppage of the game.You can really see the "Facility Staff as Game Developer" Metaphor shining through at the end of the game. The staff in the Facility behave very unnaturally; while some of them are screaming and running from the Blob and trying to impede his progress, others are passively observing and at times, trying to help or direct the Blob. (Incidentally, the Blob himself could represent the entire collective of Players who've managed to make it to the Final Level.) The entire Final Level in the Facility itself is nothing more than a part of the game where the artificiality of the constructed game world is most apparent. The puzzles that the Blob must solve to advance have conveniently grown large enough to pose a challenge to him. There's even a diorama in one of the Facility rooms that the Blob falls into, that shows the Ending Point of the game where the Blob eventually ends up. At the end of the game, the Player loses control of the Blob not because it dies or takes control from the Player, but simply because it's the End of the Game. The Player's time in the game world has come to an end. The Secret Ending exists only as an enticement added by the Developers, - one last chance to get their message to the Player declaring that the Game is a metaphor for the game development and playing process. Once the Boy tears out the cable and loses the ability to move, the message is received, and thus, the game ends.

The Blob Monster is the collective consciousness of humanity
The game takes place in a invasion of the body snatchersish future in which alien parasites have taken over the bodies of all people and some animals. These parasites have transferred the original minds of the bodies they inhabit to the giant fleshy body seen in the game and when a parasite is removed from the original body the host body becomes a inert shell because there isn't any mind existing inside of it. The boy is the last person to not have been body snatched and is trying to rescue the rest of humanity from the facility where its being kept. The reason everything in this world is so muted and industrial is that these parasite seek technological advancement above all else. Perhaps they seek to expand their influence to even more worlds and are researching the technology to make the trip. Unlike invasion of the body snatchers the parasites do have emotions but their perspective on the world is very different from that of people.

The game is a prequel to A Wrinkle in Time
In A Wrinkle in Time, the protagonists journey to a planet where everything and everyone is controlled by a giant brain called "IT". The Blob, in the water, is hooked up to the mind control helmets used to control things that may or may not be people, and also looks a lot like a giant brain. Clearly, this game takes place on Camazotz, and the scientists are trying to develop and create "IT", of which the Blob is a prototype.

The CEO wants the boy captured alive.
Some of the ways that the player character can fail appear to be attempts to simply capture them rather than outright kill them. The armed guards shoot tranquilizer darts rather than bullets, and the unarmed guards use what looks like chloroform on the boy rather than choking him (they grab the boy by the face rather than the neck). Also, the spotlight drones shoot what looks like some sort of taser, paralyzing the boy and pulling them away, possibly to be brought to a security officer. As for guards that use the attack dogs, they could either be Too Dumb to Live (if killing the boy would result in the guard in question being disposed of), or they could have their own personal reasons.

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