The Captain acquires a new weapons system from an Entharan trader named Kovin, and Seven of Nine is asked to help with the integration. When Kovin criticizes her work and pushes her aside to do it himself, she hits him. After Seven exhibits newfound anxiety in sickbay, the Doctor believes it is caused by blocked memories trying to surface. He has added a psychiatric subroutine to his program and leads Seven through hypnotic regression therapy. During their session, Seven recalls that Kovin performed a medical procedure on her and extracted Borg technology.

While probing her memories, Seven remembers the procedure took place while she and Kovin were testing weapons. They entered his laboratory, and he fired a thoron beam at her. Then, he activated the assimilation tubules in her arm and extracted some nanoprobes. Another Entharan was lying on the next table, and he was successfully assimilated with the nanoprobes. Janeway questions Kovin, who denies everything and claims the thoron weapon was fired accidentally. Faced with contradicting stories, Janeway proceeds with an investigation.

Kovin pleads with Tuvok to drop the charges against him. Since his people depend on trade, just an accusation of violating their protocols concerning diplomatic relations is a serious offense. Kovin knows he will be ruined. With the Entharan magistrate's help, the Doctor inspects Kovin's lab and finds a sample of Borg nanoprobes on his table. Informed that this is sufficient evidence to detain him, Kovin immediately transports to his ship and escapes.

In pursuit of Kovin, Janeway and Tuvok continue to inspect his confiscated weapons. When they simulate a thoron blast to Seven's arm and study a tissue sample, they find that her nanoprobes regenerate just as they did in Kovin's lab. It appears to be a spontaneous response to the thoron blast. They suddenly realize that Seven's repressed memories are most likely images from her experiences as a Borg that she confused as Kovin.

When Janeway hails Kovin and explains they made a mistake in accusing him, he thinks it is a trap. He begins firing at Voyager, but Janeway refuses to return fire and tries to beam him aboard instead. As Kovin overloads power on his ship, it destabilizes and explodes, killing him. Seven experiences remorse, as does the Doctor. Believing that his overzealous enthusiasm for expanding his program resulted in the tragedy, he requests permission to delete everything except his original activation program, but he is denied.