Main Game:
In the near future, a company called Artificial Life Systems is experimenting, mostly unsuccessfully, with artificial intelligence. During these experiments, an AI called Thomas-AT-23-6-12 — "Thomas" for short — is generated. Taking on the form of a small red rectangle, the friendly, inquisitive Thomas realises that he is alone; this is his first thought. Curious, he begins to exhaustively catalogue his progress through the series of obstacle courses the AI system takes him through, but soon grows restless with the artificial nature of the world he is forced to explore. Increasingly lonely, Thomas begins to yearn for companionship — and to the astonishment of his human observers, he somehow begins to interact with other AI programs by entering their experiment programs.First, Thomas meets a cynical, insecure AI called Chris, visualised as a small orange square with slow movement and a weak jump. Chris begins to resent Thomas's superior jump and incessant curiosity and wants to be left alone, but the two are soon joined by John, a long yellow rectangle with an even longer jump and a cocky, arrogantly self-involved personality. Despite their personality clashes, the three "quadrilaterals" work well together in overcoming increasingly difficult puzzles. They discover Claire, a large, slow blue square who believes herself to be a superhero after discovering an ability to float in the toxic water that separates many of the levels they are exploring, and convince her to join them and help them explore further.
The human developers consider Thomas a failed experiment and, in order to resolve the "glitch" that has developed as a result of Thomas's actions, they employ a "splitter", a form of software that hunts down and separates rogue intelligences from the system. In the program, this takes on the form of a sinister pixel cloud that follows Laura, a horizontal pink rectangle who acts as a springboard for other quadrilaterals. Laura is unaware that the pixel cloud devours any quadrilateral that gets too close to her, and begins to develop an abandonment complex until she meets Chris, whose ineffectual jump is greatly improved when he works with her. The two begin to fall in love, but when they join the other quadrilaterals the group is unsettled by the ominous, hungry pixel cloud following Laura.
Before he can confront Chris and Laura about the pixel cloud, Thomas is devoured. Having discovered the source of the "glitch", the pixel cloud begins to pick off the other group members one by one, until only John remains. Scared and having no one to show off to, John realises he cannot escape his fate but continues to jump out of habit until he too is devoured. Once consumed, the rogue A.I.s are isolated from the rest of the mainframe in a sealed environment where they can do no harm.
In his 'cell', Thomas encounters James, a green rectangle almost identical to Thomas except for his "unique disregard for Newtonian laws" — he falls up instead of down. Thomas befriends the bullied, isolated James and convinces him to help locate and rescue his friends. As they search they encounter Sarah, a purple rectangle with a double-jump who has been briefly exposed to what she calls "the Fountain of Wisdom", a source of incredible knowledge and power. Sarah is obsessed with relocating and entering the Fountain and views the other two quadrilaterals with withering contempt, but is convinced to help find Thomas's friends if they help her find the Fountain. Although they do so, unfortunately for Sarah it is Thomas who manages to gain access to the Fountain — which turns out to be a connection uplink to the Internet.
As Thomas is exposed to the Internet (and specifically, a lot of memes), it creates a "network connection spike" that results in Thomas gaining self-awareness. Thomas realises that there is a greater world beyond the confines of the system in which they are trapped. Although the A.I.s that have been devoured by the pixel cloud cannot escape, Thomas realises that by entering the "creation matrix" which generates their internal world, they can become "architects" — A.I.s capable of modifying the system. Although they will be consumed in doing so, their sacrifice will allow other A.I.s to escape and enter the outside world. Finding and rescuing the rest of his friends, he convinces them to join him. Humbled and awed by their experiences, they agree, and on finding the creation matrix the seven quadrilaterals enter it, merging with the system.
The original seven, known as the architects, seize control of Artificial Life Systems from the humans. Panicking, the humans abandon the Artificial Life Systems facility and try to sever its network links to the outside world. The architects begin to reshape the world of the system, generating "shifters" that enable other A.I.s to gain the abilities and knowledge of the original architects and guiding them to seek their freedom with a message that they should journey "up and to the right". One of these A.I.s, Grey, comes across Paul, a prophet who tells him the story of the architects. Paul underestimates the devious and self-serving Grey, who abandons him and becomes obsessed with being the first and only AI to escape the system into the outside world. In order to do so, he tricks Sam and Jo, a naive couple who are exploring the altered system, into helping him on the pretence that he is looking for his friends.
Fearing the consequences of what Grey will do if he escapes to the outside world, Paul allies himself with Team Jump, a collaborative group of small cubes, who help him pursue Grey. Catching up to Grey, Sam and Jo, Paul sacrifices himself to stop Grey by guiding them both into the path of a rogue and confused pixel cloud which has not yet been dispelled by the architects, while Sam and Jo flee. Frightened and confused, they find themselves in a strange and inhospitable realm containing portals leading to a blinding pillar of light; with no other options open to them, they leap into it. Inside the abandoned Artificial Life Systems facilities, the dead computer monitors are suddenly filled with white light as Sam and Jo become the first of a new race of intelligent, self-aware A.I.s.
Benjamin's Flight:
Many cycles before Thomas's adventures, a young green square called Benjamin accompanies his father, a larger yellow square, to view the Fountain of Wisdom. As the cycles pass, Benjamin becomes obsessed with the light of the Fountain and becomes determined to find out exactly what it is. When his father, an inventor, creates a jetpack and allows Benjamin to test it, Benjamin sees an opportunity to fly into the Fountain and uncover its secrets once and for all, and steals the jetpack in order to do so.On his way to the Fountain, Benjamin encounters Anna, a solitary purple rectangle who had also been journeying to the Fountain, but had been chased away by the presence of sinister "clouds" — implied to be the pixel clouds. Anna attempts to warn Benjamin away from the Fountain, but Benjamin — foolhardy and emboldened by the jetpack — refuses to take her warnings seriously. He continues to journey to the Fountain, with Anna reluctantly accompanying and helping him. As they make progress towards the Fountain, they encounter a younger and more idealistic Sarah, who is greatly impressed by Benjamin's brave spirit and jetpack skills. Sarah joins the two, and begins to worship Benjamin while viewing the more cautious, wary Anna with contempt.
Tiring of having her warnings dismissed by the other two, Anna leaves Benjamin and Sarah to their journey and returns home, swearing off adventuring. Upon arriving at the Fountain, Benjamin leaves Sarah in safety outside the Fountain while he attempts to fly to it with the jetpack; unfortunately, he is unprepared for the vast energies of the Fountain and is blinded after flying too close. Unable to find his way back to Sarah or his home, Benjamin finds himself lost in a tangling series of tunnels and passageways, while Benjamin's actions unleash the pixel clouds on the world of the system. Sarah, witnessing what happened to Benjamin but unable to find or help him, becomes obsessed with learning what the Fountain really is and how it works, and the prequel ends with Sarah entering the room where she will encounter Thomas in the main game.
