SPQR is a 3D adventure game that challenges you to learn how the Roman Empire works - structurally, mechanically, economically, culturally and politically. Players are given one year to investigate five equally suspicious suspects in order to solve the ultimate mystery: Who is plotting to destroy Rome and how will they do it?

The player is an unnamed character, a friend of the inventor Cornelius who has been arrested. His arrest was on the suspicion that he is involved with the Calamitus, a figure who intends to destroy Rome. The game starts underneath Cornelius's workshop, and once the player has entered the workshop itself they receive a message about his arrest. The message also gives the names of five possible Calamiti:

Lucius: A retired soldier who is now a private investigator. Whilst not investigating, he spends his days drinking in the wine shop below his flat.

Verania: The head Vestal Virgin, who is thinking of retirement.

Xanthus: One of Gordian's assistants who claims to be Greek, but is actually a barbarian.

Sybil: A prophetess who runs a small stall, but later works for the Roman Emperor.

Gordian: An architect who is using the spare money from projects to build his own temple.

The player is also told about the Navitor, a machine that allows them to wander around Rome in the comfort of the workshop. Once activated it can pick up objects and use them in other places, travel in time and view each of the suspects' diaries.

When the player has activated the Navitor, their first task is to find the suspects' diaries. After this, they automatically update. There are also 'quests' each month, consisting of a screen shot. The player must find the location portrayed in the screen shot and complete a puzzle or task to gain more clues and/or an important object. The events in Rome can be read both through the diaries and in the city newspaper, and can often help with the month's quest. Occasionally, the Navitor will crash, and the player must fix one of the machines around the workshop in order to fix the Navitor itself. Each of the machines represents a season, and only the correct machine for the season can be fixed.