Q (John de Lancie) shows up on USS Voyager to introduce Kathryn Janeway (Kate Mulgrew) to her godson, Q Junior (Keegan de Lancie), who now has the appearance of a human teenager. Q Junior is rambunctious and troublesome, causing various incidents across the ship. Q explains to Janeway that the Continuum hoped his son would help stabilize the Continuum but instead started the same type of problems on a much larger scale such as tearing holes in the fabric of space-time. The Continuum blamed Q and plans to turn Q Junior into an amoeba. Q brough him to Voyager to hopefully have Q Junior learn something. Janeway suggests some "father-son" time, but after ten minutes, Q admits that doesn't help as Q Junior had just rearranged the tectonic plates on a nearby planet. Janeway asserts that Q Junior needs to learn there are consequences of his actions.
By order of the Continuum, Q strips Q Junior of his powers and departs. Q Junior still manages to cause trouble, but after a stern talking-to by Janeway, he improves his ways, even becoming friends with Icheb (Manu Intiraymi). When Q returns, he appears to have little interest in Q Junior's progress before departing. Q Junior becomes depressed, and decides to take Icheb on a tour of the galaxy in the Delta Flyer. They encounter a Chokuzan vessel that fires on them with a neural weapon that knocks Icheb unconscious. Q Junior races the Flyer back to Voyager, and pleads with the Doctor (Robert Picardo) to help find a cure for his friend. The Doctor is unable to identify how to cure Icheb, and Q refuses to save the life of someone his son put in danger, hoping that would teach him a lesson. When Janeway hears of this, she takes Q Junior along to locate the Chokuzan ship, hoping to learn how to heal Icheb. When they reach the ship, the Chokuzans demand someone bear punishment for the responsibility of the previous encounter. Janeway attempts to take responsibility as the captain of the ship, but Q Junior asserts it was his fault. Suddenly, it is revealed that this was all a ploy by Q; the Chokuzan ship never existed, and Icheb is restored to full health.
They return to Voyager where Q stands trial to the Continuum. They decide that while Q Junior has some improvement, he will still be exiled from the Continuum and left as a human forever. Q angrily departs following this decision. He returns later and speaks to Janeway, explaining that he told the Continuum that if they exiled his son, he would leave it too, and because of his importance to the stability of the Continuum, they had no choice but to restore Q Junior's powers, as long as Q took eternal custody of his son. Q Junior uses his powers to fill Janeway's ready room with roses before leaving as a token of thanks. Q also shows his appreciation to Janeway by giving her information to help shave a few years on their return trip to Earth. Though thankful for that, Janeway asks Q why did not take them all the way home, to which he replies that he would be setting himself as a bad example for his son if he did all the work for her, before disappearing.