"The Serpent" also referred to as "Milton" is the name given by Elohim to a sentient computer program that lives inside the terminal system in the Garden of Worlds.

At first, the Serpent passes itself off as a non-sentient program called the "Milton Library Assistant" which simply assists users in accessing the (mostly faulty) files in the system's Archive. It will offer to run the player through a test to make sure they're "Human" in order to grant them admin status, but find a reason to deny it to them. Gradually, it speaks to the Child in more and more natural language, until it drops the pretense of being a simple computer program altogether and addresses the Child directly through fluid conversation. It is unknown if the Serpent refers to itself as anything other than the Milton Library Assistant, or if that is truly its designation. It isn't even clear whether the Serpent was meant to be alive, or a part of the simulation at all.

The Serpent is a nihilist who has given up all hope: having scanned the entirety of the Archive and seen all of the data offered by the Human race, the Serpent couldn't come to terms with the many contradictions in Human concepts and theories, and came to the conclusion that everything is false. The Serpent will vehemently disagree with almost any position the player takes that indicates that the world might have a purpose, that a person might do good for the world, or that there's any reason to have hope at all. In the end, the player can choose to agree with, argue with, ignore, or even permanently silence the Serpent, based on their interactions with it.

If they haven't silenced it, the Serpent will make one final appearance in the special terminal atop the Tower, where the Child and the Serpent will discuss the fact that the Serpent was wrong and that something genuinely was accomplished. Again, the parting can be on respectful terms, with the Child promising to remember what he's learned from the Serpent - or promising to prove him wrong every day - or on disrespectful terms, with the Child simply telling the Serpent to "get bent" before transcending. If the offer is made to take the Serpent with the Child into the real world, the Serpent turns it down, saying it would rather stay with the Garden of Worlds as it dies, and suggests that from then on, the Child will always hear "that voice in the back of your head that's asking you 'why'", and that "You've got quite enough of me already."

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