Most of the crew on the ship are dead however there are several 'passengers,' who do survive. With the help of a new recruit who did survive, Harry manages to get main power back online. However the passengers seem more worried about getting their clocking device back online than treating the wounded.
Meanwhile Voyager is sat on a planet making repairs to the ship, in particular its warp drive. B'Elanna offers to take Icheb, one of the rescued borg children, rock climbing once the repairs have been finished.
Back on the shuttle the alledged doctor (who is head of the passengers) asks Harry to help them by captaining the ship back to their home planet as they have never flown a ship before. Harry agrees to take them as far as Voyager which is on the way to the planet.
When the ship reaches the planet which Voyager is currently sitting on, they find 3 Antarie vessels in orbit and unknown to them, Anatarian's chatting to Captain Janeway as she discusses the possibility of trading with them.
Once the Antarie leave, the aliens and Harry head down to the surface where they meet with Captain Janeway and explain the situation. Janeway is angry at Harry at first however Harry persuades Janeway to let him command the ship as he returns the aliens to their home world.
Icheb goes to sick bay to fix a broken holo emitter which causes The Doctor's legs to disappear when he moves to the far corner of the room. He askes The Doctor above how to tell if someone is in love with you. The Doctor suggests physical responses like higher dorpheen levels.
Tom wants to join Harry on his mission as he wants to get back into space however Harry refuses as he wants it to be his mission and Tom outranks him. "You have always been Captain Proton and I have always been Busta Kinkade," as Harry put it.
Harry arrives on the brige of the alien ship and after discovering it has no name, he names it 'Nightingale' after the famous nurse due to the vessel being a medical transport or so he has been led to believe. The ship heads off into space. Harry feels like he is settling in well to his role as captain although Severn suggests he is in overkill mode.
Back on Voyager, B'Elanna and Icheb are working in a Jerry's tube continuing with their repairs. Icheb turns away to conduct a quick scan of B'Elanna's bio signs to she what she is feeling.
On the shuttle a glitch temporarily takes the cloaking device the ship has offline. The alien doctor seems very concerned at his however Harry says he will monitor it closely and seems confident to go on with the mission.
Later an explosion in engineering knocks Seven and one of the passengers working their to the ground. It takes the cloaking device offline and almost immediately Anarie war vessels are attacking the ship. Dayla, another one of the passengers is sent down their and gets everyone out as well as getting the clocking field back online however life support fails for a short period and she dies.
When asking the alien doctor to examine Seven who appears to be in shock, Harry discovers that he is not a doctor at all and knows a lot more about cloaking devices then he wanted Harry to know. After some questioning Harry discovers that the ship is a prototype for a cloaking device which will be used for military purposes.
Harry is outraged and gives the order for the ship to be turned around to head back to Voyager. However the crew refuses to follow orders and Harry is relieved of command by the head alien.
Back on Voyager Icheb reverals to B'Elanna that he believes she wants a romantic involvement with him. B'Elanna denies this even when Icheb reveales that her bio scans suggested a state of arousal. B'Elanna decides the best thing to do is play along and agrees to end their 'relationship.'
Harry moans to Seven about what has happened and has prepared an escape pod for the two to leave in however Seven tells him to stop being so studpid and to get back helping the crew make it to their home planet. Harry arrives back on the bridge to take command as they prepare to attempt to evade scanning pulses designed to illuminate cloaked ships hulls.
Aboard Voyager, Captain Janeway is hailed by two Anarie warships who say they have discovered Voyager is helping the aliens and are here to escort Voyager to the edge of Anarie space. Janeway says the warp drive is offline however the Anarie persist and say they will escort Voyager at impulse.
With the alien shop heading towards the surface and taking heavy damage Harry sends out a hail offering to surrender. Harry negotiates to get the passengers to the surface in escape pods so even if the vessel is destroyed the scientist will survive the build another one.
Seven and the new recruit alien say aboard the ship and wait for the Anarie to lock onto the ship with a tractor beam then use their own weapons against them to break free and make it to the surface of the planet.
Voyager is escorted out of Anarie space by the two ships which leave. They are about to start scanning for Harry when they receive a hail from him. The vessel is cloaked and flying just on the side of Voyager.