Lieutenant Commander Data, while practicing acting in an Enterprise holodeck, is surprised when the Orient Express train drives through his set of Shakespeare's The Tempest. Later, the Enterprise suddenly jumps into warp on its own; subsequent investigation shows that the ship had been undergoing a deadly theta flux distortion, and only by jumping into warp was the ship saved from destruction. Data postulates that this may be a previously unknown safety feature of the Enterprise, and he and Chief Engineer La Forge investigate the ship, soon discovering one of several small nodes connecting the various ship systems within the ship, all protected by their own force fields. The bulk of the nodes connect to the holodeck, and the crew go to investigate.

Inside, they find themselves on the currently-running Orient Express simulation, where several random characters are interacting in strange manners. Data attempts to shut the program down to no avail. As they watch, a gangster character shoots and kills the train's engineer, and the conductor pulls on a cord; the Enterprise is suddenly sent into warp again. On leaving the holodeck, the crew finds many more of the nodes about the ship, connecting all the major systems save the main computer; Data believes the formation of the nodes are similar to the human brain's structure, and posits that the Enterprise is developing its own intelligence.

Data, Worf and Counselor Troi return to the holodeck to learn more. The gangster character takes a brick from the engineer and gets off at the next stop - Keystone City - which the three follow. The gangster places the brick in a wall, completing it; at the same time, La Forge detects a power surge in a cargo bay and finds a strange object being constructed atom by atom. Data attempts to access the holodeck circuits, but this causes the ship to shake violently. Troi believes that the characters are trying to act out various roles in the creation of a new entity, and Captain Picard agrees with letting the simulation run its course and the object in the cargo bay, considered to be a new lifeform, to develop.

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