In the game, the player controls one or more simple rectangles representing several out-of-control artificial intelligence entities, working with the shapes to get each to their individual end points on each level.

Thomas Was Alone takes place within a computer mainframe, where some unspecified "Event" has caused several artificial intelligence routines to run out of control and gain personality.

He meets other AIs, each with different personalities and abilities: the cynical Chris, the show-off John, the self-proclaimed superhero Claire, and the apprehensive Laura.

The pixel cloud is revealed to be a "splitter", a mechanism that attempts to fix the fact that multiple AIs are erroneously being placed in the same virtual space.

Some time later, other AIs, all in different shades of grey, emerge and start using "shifters", coloured patches that equip them with one of the skills of the original seven architects.

Although Paul and Team Jump are somehow left behind along the way, Sam and Jo find and leap into the final portal and enter the outer world.

Thomas, Chris, John, Claire, and Laura (and to a lesser extent, James and Sarah) are immortalized in history as the original architects who allowed this to happen.

[2][5] Bithell continued to use rectangular characters, in part due to the inspiration of Piet Mondrian's minimalist works, and to keep the stacking mechanic relatively simple.

[5] Considering the story and gameplay design aesthetics used by Valve in their games, Bithell wrote a script to give each of the rectangles a personality and add some humor inspired by Douglas Adams and Danny Wallace.

[5] Wallace himself is the game's narrator, a result of Bithell requesting the humorist's participation in the project after struggling to find equivalent voice actors.

[5] Housden initially had trouble in considering the arrangements for the game when he envisioned the characters as simple rectangles, but when he started attaching more humanlike attributes to them, he found it was much easier to compose the music towards these feelings.

[9] Bithell credits Sony UK's senior business development manager Shahid Ahmad for helping to bring Thomas to the PlayStation consoles.

In 2012, Ahmad was looking for content for the PlayStation Vita, and after encountering the April Fools' trailer for the game he reached out to Bithell, considering his novel use of marketing to be of interest.

[11] He was also assured that the iOS port was a proper move after making sure the game felt right on the touch-screen device and did not feel like a money grab.

[12] The additional content for the PlayStation release was made available for free for owners of the Windows, Mac OS X, and Linux versions of the game on 26 June 2014.

[14] In September 2016, it was announced that Bithell and distributor Limited Run Games would release a physical version of Thomas Was Alone for the PlayStation 4 and Vita.

[15] Thomas Was Alone received positive reviews from critics, praising the use of narration to give otherwise simplistic shapes personalities, and the careful introduction and pacing of puzzles to create a smooth learning curve over the otherwise short game.

[32] As of April 2014, Bithell states that Thomas Was Alone has sold more than 1 million copies, not including free downloads during its appearance on the PlayStation Plus program.

[35] Bithell stated that he had received criticism from some players about the simplicity of the game's concept, based on the idea of just stacking rectangles.