The crew of Voyager comes across a merchant named Abaddon who is selling all sorts of items in his derelict ship junkyard. Through the search of the junkyard, Ensign Tom Paris comes across a shuttlecraft that he thinks is a real beauty and is worth selling off his jukebox to acquire. During his restoration of the derelict ship that he named Alice after a girl in the academy that wouldn't give him the time of day, Paris tries out the neural interface briefly before the ship loses power. After he goes to bed, the ship comes to life again, having used the neural interface to scan Paris' mind and create a female persona that would interact with him. Over the course of the next few days, Paris' relationships with his closest friends and with Lt. B'elanna Torres would deteriorate as all of his attention would be fixed on Alice, with B'elanna jokingly referring to the ship as "the other woman". However, when B'elanna notices that some important key components of Voyager have been stolen by Paris to fix up Alice, the shuttlecraft responds by sealing her up inside and cutting off all the oxygen. Paris soon realizes that the Alice persona now has a hold on him and tries to escape its grip, but it forces Paris to leave Voyager on a course that he has plotted for the ship: straight into a particle fountain, which is considered dangerous. With the help of Abaddon, who turns out to be a former victim of Alice, the crew of Voyager manages to rescue Paris from the ship by having B'elanna serve as a mental distraction for Paris before it is destroyed by the particle fountain.
This episode provides examples of:
- Battle in the Center of the Mind: The Doctor figures out how to insert B'elanna into the neural link between Alice and Tom, so she can talk (or yell) some sense into him.
- Call-Back: Abbadon bought the ship from a Haarkonian, the same species that conquered Neelix's homeworld. Either Science Fiction Writers Have No Sense Of Distance again, or Alice was forcing the Haarkonian pilot to take her way off his home turf. Abbadon thought he'd gone Gone Mad From The Isolation, so this could well be the case.
- Chekhov's Gun: The beryllium crystal that Neelix and Seven find in a bunch of junk purchased from Abaddon is later used as a bribing tool to get Abaddon to reveal more information about Alice, since the beryllium crystal turns out to be a valuable trinket.
- Companion Cube: Tom Paris and Alice, particularly when the ship produces a female avatar he can interact with. At the end of the episode, Tom Paris had to renounce future relationships with other spacecraft, telling B'elanna that he and the Delta Flyer are just good friends.
- Death Glare: Literally—Alice's glare almost makes Tom's head explode.Jim "Reviewboy" Wright: She gives Tom the kind of skunk eye Janeway is famous for. And unlike the legendary Janeway glares-o-pain, Alice's actually does some serious physical damage. Tom's massive forehead becomes a spider's web of overtaxed blood vessels. His scream of agony would give Jamie Lee Curtis a run for her money.
Everyone on Voyager has a purpose, and a unique talent. Tom's is to sound utterly convincing when he's being folded, spindled and mutiltated. Nobody—and I mean nobody—screams like Helm Boy.
- Evil Costume Switch: Tom Paris goes from wearing his Starfleet uniform to wearing a dark grey flight suit as he gets further and further controlled by Alice — not that he completely turns evil, but he does things that he says would get him busted down from Ensign to Cadet. He also notably forgets to shave.
- A Form You Are Comfortable With: Alice projects herself as an attractive woman that only Tom can see. Abbadon sees her as a woman from his species as well.
- Got Volunteered: Tom claims that Harry volunteered to help restore Alice. Harry is not amused.
- Homicide Machines: Alice tries to kill B'elanna Torres by sealing her up inside the ship and cutting off all the oxygen. It also tries to do the same to its pilot Tom Paris by having him drive the ship into a particle fountain.
- Honest John's Dealership: Abaddon's Repository of Lost Treasures, where "all trades are final".
- I Call It "Vera": Apparently, Alice is named after a girl from the Academy who Tom was attracted to, but who wouldn't give him the time of day.
- Icarus Allusion: When Alice tells the story of Daedalus escaping the labyrinth, she leaves out the part where Icarus falls to his death. Tom calls her out on that.
- Infinite Supplies: Chakotay is reluctant to purchase Alice because they already have "a full complement of shuttles" despite having lost several in previous episodes.
- Inspiration Nod: The shot of Alice alone in the shuttle bay suddenly lighting up is a clear Shout-Out to a similar scene in the film version of Christine.
- Karma Houdini: Abbadon sold Voyager a ship he knew was intelligent, homicidal, and capable of mind control. Not only does the Voyager crew save his life and undo her link to his brain, they even trade him a crystal worth a fortune to get him to talk, meaning he came out of the whole thing rich.
- Mind Rape: Alice inflicts control over its pilots by appearing as female avatars of their native species (as in the case of Abaddon and Tom Paris) and causing brain hemorrhages to keep them in line.
- Murder the Hypotenuse: Alice tries to kill B'elanna by trapping her in the ship and cutting off the oxygen supply so she can have Tom for herself.
- Negative Space Wedgie: The "particle fountain" that Alice almost makes Tom fly into. A similar one destroyed a dozen ships in the Alpha Quadrant.
- Not So Different: Alice is a lost ship trying to get home, just like Voyager.
- Plot Hole: It is revealed that Alice once interfaced with Abaddon and forced him to find it a new owner. When it is sold to Voyager, it is completely deactivated — completely vulnerable.
- Recycled In Space: Christine as a shuttlecraft.
- Ribbon-Cutting Ceremony: Tom Paris replicates a bottle of champagne for the christening ceremony of the nearly-complete refurbished Alice. However, with B'elanna's prompting, Tom decides to share a toast to the shuttle with her instead of breaking the bottle on its hull. They do manage to spill a bit of champagne upon the upholstery inside the shuttlecraft.
- Say My Name: B'Elanna shouts "Tom Paris!" when she goes to find him after she gets a clue that he's stealing parts from Voyager to fix up Alice.
- Spaceship Girl: Alice chooses to present itself as an attractive woman to the pilots she mind controls.
- Suddenly SHOUTING!: When B'elanna escapes suffocation and confronts Tom about his behavior, Tom responds with heaping helpings of this (being mind-controlled and all).Tom: LISTEN TO ME!!
B'Elanna: Are you out of your mind?!
Tom: STAY OUT OF THIS, B'ELANNA!
B'Elanna: Or what? You'll sic Alice on me again?
- Synchronization: With Tom and Alice linked, firing on Alice hurts Tom as well.
- Time-Passage Beard: Tom goes a few days without shaving and grows a small beard.
- Title Drop: The title is the same as the frequently-referenced-by-name ship.
- The Un-Reveal: So why was Alice so hell-bent on getting to that particle fountain, anyway?
- Vague Age: Tom Paris and Harry Kim have fun trying to guess Tuvok's actual age, which he refuses to divulge. (Considering that this information should be in some Starfleet records, they're probably doing it just to mess with him.)
- Whole Plot Reference: To Christine, complete with the episode being named after the malevolent vehicle and said vehicle attempting to kill her owner's girlfriend.
- Worthless Yellow Rocks: The random junk Abaddon cons the crew into buying includes a beryllium crystal. He and the crew dismiss it as worthless, but Seven reveals that in a nearby section of space that uses such crystals as currency it represents enough wealth to purchase an entire fleet.
- Yandere: Woe befall whoever stands between Alice and her pilot.