In a post-apocalyptic world, android Horatio Nullbuilt (Logan Cunningham) and his floating robot companion Crispin (Abe Goldfarb) inhabit and attempt to rebuild U.N.N.I.I.C, a derelict airship stranded in a vast desert.

At entry, Horatio is stripped of a megacycle (CPU power cycle) and the 'Gospel of Man', deemed a subversive literature that is tossed into the city's underground, the Underworks.

In the back of the courthouse, Horatio finds the corpse of Clarity's sister and fellow legal aid, Charity, and obtains her final memories.

Charity's memories reveal evidence that MetroMind used her to be rid of Arbiter – under the pretense of "preventing a civil war" – and take over Metropol through a silent coup.

Witnessing this, Clarity determines MetroMind has lost all legal protection and joins Horatio and Crispin's quest for the power core.

She informs Horatio that in order to confront MetroMind, they must acquire fragments of the access code to MetroTower, which was exclusive to the ruling AIs.

Memorious took sides with MetroMind with the removal of Steeple for calculating the data regarding humans felt irrelevant to city administration.

The trio also learns that humanity extinguished themselves in chemical warfare between its four remaining cities (Municipa, Civitas, Urbani and Metropol), leaving only machines behind.

In the Underworks, the trio reactivates Factor, disabled on MetroMind's orders, and Horatio recovers the Gospel of Man confiscated from him.

Upon reactivating, Horatio recovers a data chip from MetroMind's mainframe and discovers his true identity as the AI of HORUS, an Urbanian war machine unleashed to destroy Metropol.

However, as HORUS attempted to destroy all human life in Metropol, its last name "Manbuilt" made him realize he was targeting his own creators.

Horatio spreads the Thanatos virus to MetroMind's broadcast system, throwing Metropol into irreversible chaos, but avenging the extinct humankind.

However, if neither party member is present, Horatio instead gives in to despair and wipes his memory like his previous versions did; there is no ship repair scene or other robots in this ending.

Adventure Gamers described Primordia as "a gorgeous, clever, and melancholy science-fiction parable" with "beautiful, surrealistic retro graphics [that] drip with atmosphere.

"[10] The site also awarded it Setting of the Year for its "haunted world, one that oozes history far more detailed than the events laid out by the game's exposition, and one that stuck with us long after we left it behind.

[8] TouchArcade rated the game 4.5/5, describing it as "brilliant": "The writing is stellar, the voice acting is ace, the style is top notch, and the soundtrack perfectly sets the tone.

"[20] In June 2013, Wormwood Studios released "Fallen", a spoiler-free spin-off story set after the game's ending,[21] which was praised for its writing and art.