Voyager is traveling on its long journey home when the ship is rocked by a shockwave caused by polaric ion energy from a nearby red dwarf system. The ship moves to investigate and discovers an M-class planet. There is no life on the planet, but there is evidence of a former civilization. Janeway leads an away team to investigate. They find the remains of cities, which apparently used the volatile polaric ion energy as a power source. Paris locates a clock that is stuck on the time the apocalyptic explosion went off. However, he starts to phase back and forth in time, seeing the civilization before it ended. Before Janeway can order everyone back to the ship, she and Paris are marooned on the planet before the catastrophe.
While this is happening, Kes has become distraught, believing that she saw psychic images of the civilization's destruction. She believes that it signals a return of the psychic abilities her species, the Ocampa, are said to once possess. Neelix doubts the stories, but Kes is adamant. She gets her brain scanned by the Doctor, but since he has no frame of reference on her species, he cannot give her any useful diagnosis.
On the planet, Paris and Janeway work to fit in, but Latika, a young boy who saw them appear, is convinced that they're demons and starts spying on them. Paris locates a working timepiece and figures out that the world-ending catastrophe will happen within a day. They start investigating the local polaric field and trace it to a power plant, where a protest is going on. Janeway gets injured during the brawl and taken to the home of a protest leader, Makull, to recuperate. However, her and Paris's story quickly breaks down under his questions, and he and his associate Ny Terla hold them at gunpoint, believing them to be spies.
On Voyager, Chakotay leads an effort to rescue the castaways. They work on a device that will help reconnect them to their own time. Kes insists on joining the away team. While on the planet, Kes hears Janeway speak momentarily, detecting her across time. A day previously, the two protestors haul in Latika, whom they caught skulking around, and force him to join their other two captives. Under questioning, Janeway comes clean about being from the future and explains the impending calamity, but Makull doesn't believe her. Chakotay manages to send a brief message to Janeway through her combadge, which Makull simply confiscates. The protestors take a particle injector and order their three hostages to move out. When Chakotay's team manages to create a time bridge to rescue his crewmates, they've already left.
The protestors are planning to infiltrate the local power plant. Makull threatens to kill Latika if Janeway won't help them talk their way inside, but she sabotages their efforts, resulting in a shootout with the guards. The protestors try to shoot Latika, but Paris takes the shot to save him. Inside, Janeway manages to hold Makull at gunpoint and explains that blowing up the plant will destroy the world, but Makull insists that he's not there to blow up the plant. Meanwhile, Kes leads the rescue team into the factory and helps them locate the corridor where Janeway died. They start to open up another gate to rescue her.
On the other side of time, Janeway sees the bright light of the gate opening right next to the reactor and, seeing that it is almost the moment of the world-ending explosion, she realizes that it's the rescue attempt itself that caused the calamity. She uses her phaser to close the gate before it can destroy everything. In doing so, she averts the disaster that set everything in motion, and time resets to just before the explosion. No one has any memory of the events that transpired throughout the episode, though Kes seems unusually relieved to be told that the nearby M-class planet is teeming with life.
This episode contains examples of the following tropes:
- Aliens Speaking English: As per usual for this series, the universal translator works perfectly on a species on the other side of the galaxy that's never even made First Contact.
- Book Ends: The episode starts and ends with the same scene of Tom trying to convince Harry to go on a double date with the Delaney Twins. In the second scene, the explosion never occurs, Tom and Harry go to meet the Delaney Twins, and Voyager continues on its journey without stopping at the planet; since it's a (ostensibly) normal pre-warp civilization, there's no reason to.
- Call-Back To TNG's "Yesterday's Enterprise" when Kes checks with the bridge that everything is all right at the end of the episode, just as Guinan did.
- The Casanova: Tom tries to get Harry to go on a double-date with the Delaney twins. When Harry says he has a girl back home, Tom casually admits to having five, and points out that the rest of the crew will start pairing up soon, so they need to get in first.
- Changed My Jumper: Realizing they stick out in their Starfleet uniforms, the first thing Janeway and Tom do is ask for directions to a clothing store. They apparently sell their uniforms to purchase the local fashion of striped sweaters.
- Chekhov's Gun: The disorganization caused by the loss of the Chief Medical Officer, who would normally arrange to get the complete medical histories of the new crew members, becomes significant in "State of Flux".
- Complaining About Rescues They Don't Like: Janeway discovers that her crew's rescue attempt is what causes the explosion and seals it, so they are rescued in that it never happened.
- Does This Remind You of Anything?: A planet that uses a form of energy as a power source which can or does have very negative consequences, to the point there are people protesting its use and doing everything they can to sabotage it, all while the companies that produce the energy refuse to listen and even work to crush dissent against it because they don't want to cut into their profits. The parallels to both nuclear energy and the pollution/global warming dangers of fossil fuels are clear.
- Eats Babies: Invoked. A local boy starts harassing Janeway and Paris, fearing they might be demons. When he states that there are only four people coming from Kalto Province, three quarters of them were a couple and their child, so if they were them, they'd have a child with them. Exasperated, Tom says they've eaten the child; they really are demons, and that it's been a while since lunch, causing the youth to flee in terror.
- The Extremist Was Right: While their tactics are something less than diplomatic, the anti-polaric group is trying to prevent a disaster that Janeway and Paris know from being time travelers is already destined to happen. Subverted when it turns out that what caused the disaster was Voyager attempting to rescue Janeway and Paris, and the anti-polaric group had no intention of causing an explosion.
- Failsafe FailureTorres: A civilization powered by polaric ion energy?Janeway: A timebomb under every street. Running into every home.
- False Reassurance: The Doctor sardonically tells Kes she has the healthiest Ocampan brain he's ever seen. Of course it's the only Ocampan brain he's ever seen.
- Fictional Geneva Conventions: Tuvok mentions the Polaric Test Ban Treaty of 2268, which prohibits research into polaric ion energy by the Alpha and Beta Quadrant powers due to its destructive potential: a Romulan research colony was almost destroyed by an accident.
- Funny Background Event: An audible one. Paris is trying to coax Harry into a double date, and told a few lies about him, to Harry's dismay. As the scene changes to the other characters on the bridge you can still hear the two bickering about it.
- The Ghost: The Running Gag of Harry and Tom dating the unseen Delaney Sisters commences (they finally make a one-off appearance in Season 5's "Thirty Days").
- Headbutt of Love: Neelix comforting a distraught Kes after she felt the death of everyone on the planet.
- Heroic Sacrifice: Tom Paris jumped in front of Latika to protect him. Notable as Paris thought these people had less than an hour to live.
- Human Aliens: They don't even have funny foreheads! This makes it handy when Tom and Janeway have to unexpectedly impersonate the locals on a planet that hasn't made First Contact with aliens. Janeway's red hair is commented on, but that's it.
- The Main Characters Do Everything: Tom hands over the conn to a female crew member at the end of his shift, then goes to talk to Harry. After they hit the shockwave, he takes back the helm, then hands it over again to go on the Away Team.
- Microts: The clock uses rotations, intervals, and fractions... and Hindu-Arabic numerals.
- Missed Him by That Much: The activists have marched Paris and Janeway out of the room just as Voyager makes its first subspace breakthrough and tries to hail them through their badges (which are still lying on the table).
- My Girl Back Home: Kim wants to remain faithful to his girlfriend back home, Libby.
- My Significance Sense Is Tingling: Kes sleeps through the shockwave, then abruptly sits up in bed like she felt a great disturbance in subspace, as if millions of voices cried out in terror and were suddenly silenced by a planet-wide polaric ion discharge. In the reset timeline, she remembers this happening, but the planet is now normal.
- Oh, Crap!: The lead activist threatens to shoot the kid if Janeway doesn’t try to fool the guard. Janeway promptly spills the beans. The activist’s “oh crap”/“pretend it’s still ok” reaction is priceless.
- Only Sane Man: The Doctor's reaction when he realizes no-one informed him that Voyager was now carrying two alien passengers, Neelix and Kes. Oh and 36 Maquis now serve as part of the new crew. And he can't contact Captain Janeway because she's down on the planet below. Oh... and she is currently missing.Doctor: It seems I've found myself on the voyage of the damned.
- Prime Directive: Janeway forbids Tom to warn the planet about the upcoming disaster. She changes her mind when she realises they must have caused it.
- Race Against the Clock: Tom finds a Stopped Clock in the wreckage of a store. After they time-jump, he compares the time he saw to its counterpart in the past, and works out the disaster will happen tomorrow.
- Reset Button: Thanks to the Timey-Wimey Ball, Janeway preventing the polaric disaster ends up undoing everything in the previous day, and everyone's awareness of it (except for Kes, who still has at least some knowledge of the original events).
- Set Right What Once Went Wrong: When the activists move up their assault on the power plant to the day of the disaster, Janeway decides the Prime Directive no longer applies as their presence has already altered events.
- Snooping Little Kid: Latika, who turns out to be a School Newspaper Newshound.
- Taking the Bullet: Tom jumps in front of the activist shooting at Latika.
- Time-Travelers Are Spies: The activists assume Paris and Janeway come from the power company's security force and were trying to infiltrate them, as they're picking up huge polaric energy readings from them, something commonly detected only from people who've been in the power plant recently.
- Timey-Wimey Ball: The attempt to get Paris and Janeway back is what actually causes the explosion in the first place; except that this time Janeway manages to block the incursion so that the explosion doesn't happen after all.
- Walk and Talk: The activists with their guns on Janeway and Paris march them to the power plant slowly enough that they're able to puzzle out their situation a bit along the way. The terrorists make no effort to silence them, even though for all they know our heroes could be planning an escape!
- What the Hell, Hero?: Tom Paris calls out Janeway on intentionally letting an entire planet get wiped out for the sake of upholding the Prime Directive, and points out that her argument about "not knowing the consequences of intervening" is pretty absurd considering they really couldn't get any worse than the known consequences of not intervening. She admits he's right later on.
- Would Hurt a Child: The activists threaten to kill Latika if Janeway doesn't help them get inside the plant. The problem is she's not the security agent they think she is, so her only option is to tell the guard at the gate they're being held hostage. Violence ensues.
- You Have to Believe Me!: Janeway has significant difficulty convincing the activists that she's a space alien from the future rather than a government infiltrator.
- You Watch Too Much X: Latika screams in terror when Tom and Janeway appear, and screams that they must be demons because they popped out of thin air. A nearby policeman tells him that he "reads too many of those Darkstorm tales."