While flying a shuttle on his way to a vacation on Risa, Geordi La Forge is kidnapped by Romulans. Meanwhile, the Enterprise heads to the Kriosian system with Klingon Ambassador Kell. Krios, an outlying Klingon colony, is fighting for independence, and the Klingons do not wish to devote resources to such a trivial rebellion. The Governor of Krios claims the Federation is arming the rebels, and the Enterprise has been summoned to disprove the claim.
In the meantime, Geordi is being tortured by the Romulans and subjected to mind control techniques. A Romulan named Taibak removes Geordi's visor and hooks a machine directly to Geordi's visual cortex. Taibak beams increasingly disturbing images directly to Geordi's brain, to influence his psyche and effectively control him. After Geordi kills a fake Chief O'Brien in a holodeck simulation, Taibak determines that La Forge is ready to be deployed on a secret Romulan mission.
Geordi meets the Enterprise at Krios, and the crew assumes he has just returned from Risa. While doing research Data detects some E-band radiation, which is a rare phenomenon, and Commander Riker orders him to check it out.
The Governor of Krios, a Klingon named Vagh, summons Captain Picard, Riker and Kell to see him. He explains Federation medical supplies have been found in the possession of the rebels, and he is furious. He also presents a Federation phaser rifle that was discovered. This angers Worf who clashes with Vagh, believing that he has a vendetta against the Federation. Picard promises to investigate the entire situation. Geordi and Data test the phaser rifle, and discover the energy output of the gun is too efficient. They conclude that the rifle was charged using a forced pulse, which is a technique used by the Romulans.
In one of the cargo bays, Geordi reprograms some computer chips, and uses a transporter to beam down a cache of weapons to the rebels. He erases the computer memory logs and leaves. Vagh intercepts the arrival weapons and accuses Picard of smuggling arms to the rebels. Data quickly ascertains that Vagh is correct, weapons were beamed down from the Enterprise to the rebels, but has difficulty tracking down the specifics. Geordi and Data search thoroughly through the power systems. They eventually find that the power was diverted from a replicator and sent to the cargo bay to run the transporter.
O'Brien examines the transporter that was used to beam down the weapons, and finds no evidence of any tampering. He suggests the computer must have had its memory erased. Worf asks who might be capable of doing this, and Geordi responds that only himself, Lt. Kosta, Data, and O'Brien would have the expertise. The list of suspects is narrowing. Governor Vagh, his patience wearing thin, is invited to inspect the cargo bay along with Ambassador Kell and Picard to prove that the crew are being genuine and thorough with their investigation.
Ambassador Kell summons Geordi to his quarters, and orders him to kill Governor Vagh during his inspection of the cargo bay, thus revealing that Kell is conspiring with the Romulans. Data, meanwhile, detects the latest E-band transmission. He speculates that the E-Band radiation is being used by Romulan agents, and is linked in some way to the attempts to assist the Kriosian rebels. Examining Geordi's shuttle, Data finds evidence it was recently captured by a tractor beam. Meanwhile, Geordi picks up a phaser and heads for the cargo bay to kill Vagh.
Data finds that the computer chips in the shuttle also have some flaws, caused by replication. Along with the E-Band emissions, Data suspects that Geordi did not actually visit Risa and may be being influenced in some way. After discovering that Geordi is in the cargo bay, Data orders Worf, who is already in the cargo bay, to take La Forge into custody.
Seeing Geordi approaching Vagh with a phaser, Worf attempts to tackle him, but is stopped by Vagh's guards who believe that he is attacking Vagh. This leaves Geordi with a chance to get a clear shot on Vagh. Worf calls out a warning, Picard deflects Geordi's shot, and Vagh is saved. Data arrives to explain that Geordi was acting under Romulan conditioning: the E-band signals were being sent directly to Geordi's brain. When Kell demands to know who was sending these signals to Geordi, Data replies that the signals must be very close-range. Through a process of elimination, Data determines that the only two people that were close enough to send each of the E-band transmissions were Picard and Kell, and concludes that one of them may be concealing a transmitter. When Kell refuses to be searched by Starfleet officers, the Klingons take him into custody. Panicked, Kell requests asylum on board the Enterprise, which Picard denies. Vagh leaves, convinced they have found the traitor in their midst.