The game opens with a brief glimpse of Flynn's computer desk in the basement of Flynn's arcade, as previously seen in "Betrayal" Part 1 and Legacy.

The light cycle rider being pursued by two peacekeepers who all buzz past Query in front of the Repository at the beginning of the game is later revealed (in Catalyst) to be named Ter.

Query flashes to Grish his badge with an image of four squares arranged in a "T", identifying him as a member of the Disciples of Tron. The Disciples of Tron are later revealed to be an order of detective programs on the Arq Grid who follow the example of Tron by pursuing objective truth. Bound by an oath of non-interference, they investigate cases without enforcing laws or taking sides in conflicts. The four squares arranged in a "T" is the symbol that was worn on Tron's chest. The Arq Grid is soon revealed to be a backup server of the primary Grid (from Tron) created by Kevin Flynn to protect the ISOs from Clu 2 in that Grid. This Grid was left alone after Flynn's disappearance and evolved for hundreds of cycles without user guidance or interference.

Prinz asks Query who he fights for and gets the response, "I fight for myself." Wrong answer. Prinz, being a zealot who still worships the Users despite their absence for hundreds of cycles, wants to hear, "I fight for the Users." In Tron, when Flynn first sees Tron in action he's told by a Warrior, "That's Tron. He fights for the Users."

Core is the governing faction of the Arq Grid.

    Ada has a garden of plants and trees inside the Library of the Repository. The trees are said to be "data trees", growing from sustained complex computation inside a grid, with their data accessible by programs who analyze their leaves, twigs, etc. Data trees are seen not only in the Arq Grid, but also later in the ENCOM Grid in Ares. Were they also present in previous grids even though not seen?

    "Data tree" is a legitimate term in computing, generally referring to data organized in a tree structure of hierarchical nodes connected by parent-child relationships.

Ada tells Query it is a blessing he is there tonight, adding, "Flynn be thanked." This, of course, refers to Kevin Flynn, the creator of the Arq Grid and the original grid on which it is based.

Ada and Query have this exchange:

Ada: "The observation deck provides a place to meditate, to consider the knowledge collected here."

Query: "To knock on the sky, listen to the sound?"
Ada: "Ah, a student of Flynn?"
Query: "I read."

In Legacy, Flynn said to his son, "Your old man's about to knock on the sky and listen to the sound."

The suspect being held for questioning in the explosion of a vault in the Repository, Sierra, informs Query he is an ambassador for the Automata. The Automata are revealed to be a faction of ISOs in the Arq Grid who believe Users to be a myth who distract programs from attaining their full potential.

Cass is consistently referred to as "they" instead of "he" or "her", implying this program is transgender.

The narration of the story describes the landing pad at the Repository as sticking out "like a gridbug clinging unsteadily to a mountain."

The thief character called Proxy tells Query that she fought in the Adjunct War. Very little is revealed about this war, not even what it was about or which side won.

During the gameplay, Proxy will either be derezzed by Query in a disc duel or she will flee with the use of a wing chute, a device previously seen in Evolution, Legacy, and episodes of Uprising.

    Inspecting the objects in Prinz's office while he is away, Query finds a book labeled ARQ XO711 Instruction Manual. This turns out to be the User manual for the computer on which the Arq Grid is housed. Flipping through the pages and reading sections of the manual, Query remembers hearing wise programs speak of other computers, the "Many Grid" theory, and is shocked that the book seems to back that up, implying that many Users have their own computers. He finds the concept terrifying. He also finds in the book code instructions, which he thinks of as ancient runes for building programs, the way Flynn built the Arq Grid and created the programs residing in it. The recipe for life itself. PopApostle asked questions similar to this theory in the original Tron study.

    ARQ XO711 is a fictititous computer brand/model. The computer itself has a cameo in Ares, in the basement of Flynn's Arcade. According to the Tron Wiki, the ARQ XO711 is a computer that was developed by ENCOM. Possibly, ARQ refers to the abbreviation for an error control mechanism for data transmission in computing, Automatic Repeat-reQuest.

Query also finds what appears to be an action figure of Tron himself on display in the office.

Query reads a cut out newspaper or magazine article by Ethan Romero about Edward Dillinger. Edward Dillinger was the human world villain of Tron. His son, Edward, Jr., is also mentioned in the article. Junior has a cameo in Legacy and seems to be one of the subjects of "The Next Day".

A jacket of Flynn's is also found hanging on a hook next to one of Prinz's collection shelves.

Prinz continuously tries to get Query to agree to being on the same side as he, but Query seeks only truth. At one point Prinz again tries to imply they are now working together and, holding out his hand to shake, asks, "Are our operations synchronized?" This seems to be a grid version of our world's "Are we in agreement?" or "Are we on the same page?"

The Repository guard called Horii mentioned by Cass does not appear here, but does play a role later in Catalyst.

As the story is coming to an end, the narration reads, "The problems Cass has exposed will not be solved by a single hero. Those days ended with Tron."