Max learns that time is impossible to control and that her power carries many consequences as she moves inexorably towards the most agonizing decision of her life. Arcadia Bay, meanwhile, is preparing to weather a huge storm as Life is Strange comes to a gripping and gut-wrenching conclusion.

Max awakes from Mark Jefferson's drug to find herself strapped to a chair in the Dark Room alone. She desperately shouts for help but to no avail. On closer inspection of the Dark Room, Victoria Chase can be found tied up and lying on the ground beside her if the player warned her during the party and she believed. Max, desperate to find a way out, has no other solution but to travel back in time through one of the many pictures Jefferson took of her when she was drugged. There, she returns to the time where she is still drugged and Jefferon is taking photos of her. Traumatized, Max fidgets and angers Jefferson, which prompts him to increase her dosage. Hopeless to stop Jefferson, Max struggles and kicks the trolley where Jefferson keeps his photos and drugs. As the photo burns and returns Max to the Dark Room, an unhappy Jefferson is seen looking at his drenched photos.

Max, back on the chair, spots a new pile of photos on the trolley and uses a more awake photo of her taken by Jefferson to return back in time. During that time, Jefferson and Max have a little conversation where he reveals that Nathan is dead and is used as a scapegoat for his crimes. Vowing for revenge, Max pleads to Jefferson for her diary. Jefferson disregards it and throws it on the ground, which is flipped to the page with the photo Max took in Jefferson's class in Episode 1: Chrysalis. While Jefferson is going through his new pictures, Max uses this perfect opportunity to return back in time.

Back at the classroom, Max texts David about Jefferson and the Dark Room and hands in her picture for the Everyday Heroes Contest. As time passed, Jefferson is arrested and Max is seen on a plane flying to San Francisco with Principal Wells after winning the contest. However, at the Zeitgeist Gallery, Max has a vision of the storm again, but this time with Chloe's cry for help. Max leaves the crowd with a nosebleed and enters a lounge, where she checks her phone. Surprised to see her phone is on silent mode and has 6 missed calls from Chloe, she calls Chloe back immediately. A distressed Chloe tells Max that the tornado was real and is heading straight for Arcadia Bay. Realizing she didn't fix anything, she travels back in time through her contest winning picture. Inside, Max experiences another nosebleed as she learns that the "boundary" of the area is much smaller and has a similar effect of a burning picture. Deciding to fix the timeline, Max tears her contest picture, which ends her up in the Dark Room again.

Confused on what is going on, she looks around and learns that her diary is burned up by Jefferson, which made her return to the Dark Room. Victoria is also no longer there, having been killed by Jefferson. Just as Jefferson was about to kill Max, David Madsen breaks into the Dark Room, but gets ambushed and hit by Jefferson with a tripod. Using her rewind ability, Max warns David and distracts Jefferson, who is then able to neutralize and capture Jefferson. After freeing Max, David asks for the whereabouts of Chloe. The player is given the choice to either tell the truth or lie to David. If Max tells the truth, David will kill Jefferson.

Deciding to use Warren's photo to save Chloe, Max drives to the Two Whales Diner in the middle of the storm using Jefferson's car to find him. While driving, Max opens a voicemail from Nathan who apologizes and admits that he regrets his actions of dosing Kate and overdosing Rachel. He also warns Max about Jefferson before the voicemail ends. As Max nears the diner, piles of debris form a roadblock which forces Max out of her car. People rush to evacuate the town while some are heard screaming for help. Max can either help them or continue advancing forward. Among them are the Trucker, who is pinned on the leg by a wooden plank, Evan Harris, who gets hit by flying debris after being too distracted on taking pictures, Alyssa Anderson, who gets stuck in a building, and the fisherman, who is in the state of shock next to an electric wire in a flaming building. As Max advances and cuts close to the diner, fuel from a car is ignited, which blows up the diner. Using sand next to the diner, Max manages to prevent it from happening again. She enters through a side door where she finds Joyce Price, Warren, Frank and Pompidou. After chatting for a bit, Warren gives Max the picture. Before going back in time, the player is given the option to either kiss, hug or do nothing with Warren.

Back at outside the party, Max gives Chloe a hug upon seeing her. A disappointed Warren excuses himself for the two to talk. With convincing reasons, Max manages to warn Chloe of Jefferson and they both head to the lighthouse to take cover from the storm. However, just as Max is about to start walking up the cliff, she passes out and wakes up in the classroom very similar to the first episode. As the lesson goes by, red splats of blood slowly cover the window as tons of birds fall down from the sky. The moment the blood filled the entire window, everybody disappears and the window reverts back to normal. If Kate lived, the writing "I want to die" is scribbled all over her desk. If Kate died, a puddle of blood is seen on her desk. Dead birds fill the courtyard viewed from outside the window. The picture of a lighthouse now turns into a picture of the lighthouse destroyed by the tornado. The picture of the doe in the forest now turns into a picture of Chloe and Max digging up Rachel's corpse. The Everyday Heroes contest poster turns into a poster called "Everyday Zeroes" with Max's face in the foreground. The background is filled with the words "Rubbish", "Loser" and "Zero" written all over. Written on the poster is "Is Max Caulfield a loser? Does she hurt everybody she helps? YES. Max has already won because she has already lost. So don't bother to enter".

As Max tries to exit the classroom, Jefferson suddenly appears and asks her to talk about her entry before leaving, similar to the first episode. When Max approaches Jefferson, he asks Max if she would like to spend the rest of her life in his Dark Room. The options presented to Max are not what Max would say. This includes "I love you, Mr. Jefferson", "My selfies are shit", "Our dark room" and "Thanks for killing Chloe". Selecting either option makes Jefferson disappear but allows Max to exit the classroom. However, instead of entering the hallway outside the classroom, Max is now transported to the Girls' Dormitory. There, lit candles are placed in front of every room's door. Kate is seen in front of her room mourning over herself. After blaming Max for saving her/letting her die, she opens the door to her room (which is entirely white) and jumps off it. On closer inspection of the dorm hallway, a key for Room 218 is found on the desk outside the showers. Entering it changes Max's outfit to Rachel Amber's red checkered outfit and fills the dorm with her missing poster notice. Dialogue relating to Rachel is also played in the background. Entering Rachel's old room will change Max into Victoria. Similarly, her quotes and graffiti is scattered around the walls and dialogue relating to her is played in the background. Entering Victoria's room changes the player back to Max and fills the dorm with small polaroid pictures that made up her "Max Caulfield Photo Memorial Wall". Only after entering her own room does Max return to the hallway outside the class, where the same cutscene in first episode plays when she first exits class.

However, everything is reversed, with the exception of Max. Characters are walking and talking backwards while the user interface is reversed too. The music played in the background is also reversed. As Max advances, the translucent doe appears and enters the bathroom. Following the doe, Max enters the bathroom but finds herself in a dark maze resembling the San Francisco gallery with Jefferson. With her rewind ability on, Max must sneak past several clones of quite a few characters to reach the lighthouse on the other side. After the gallery section with Jefferson, a rotating statue of Principal Wells (replacing Jeremiah Blackwell) with a spotlight in his eyes in a place resembling the Blackwell Academy courtyard becomes the threat. The art in the original courtyard is replaced with pictures of drugged up victims of Jefferson's Dark Room (such as Rachel, Max and Kate), where the principal announces that Max "has died under tragic circumstances that I promise to investigate after I get my drink on". A Blackwell Academy hallway section follows shortly, with Warren, Nathan, Principal Wells, David and Samuel carrying flashlights searching for Max. Frank, Jefferson and Nathan return in the next section, which resembles the junkyard. Scattered around are bottles, which are collectibles for an achievement, but also there as a reference to the second episode.

After reaching the lighthouse, Max takes a seat on the bench next to it, only to find herself trapped in a snow globe, where she is forced to sit through the day William died. Max then appears in the Dark Room, strapped to a chair again. Jefferson and Chloe then appear in front of Max as Chloe poses for Jefferson to take pictures. Chloe and Warren then show up and kiss. Nathan and Chloe then appear sitting on the couch facing Max, where Chloe asks Max to "take a picture or take a selfie" when she sees her looking at both of them. An almost naked Chloe then appears dancing on the couch where she says to Max "No mosh pit for you, shaka brah", a reference to the third episode. Victoria and Chloe then appear and kiss. Followed after is the wheelchair-bound Chloe from the alternate timeline who appears in front of Max and blames her. The original Chloe then shows up and takes pictures of Max, similar to how Jefferson took them, blaming Max that "she is the storm" and shouldn't have come to Arcadia Bay.

Max is then transported to the Two Whales diner's restroom, where a digicode is required to unlock the door. As Max tries to figure out which numbers are correct, tons of numbers appear all over the walls and ceiling, with the exception of the mirror, which doesn't reflect any of the numbers. There, Max sees a code in the mirror and exits the restroom to find herself not alone. Every character is in the diner, though immobile, but all are begging Max not to kill them. Max finds another version of herself in the diner, the only moving person among every other character. The other Max blames and guilts the real Max, but Chloe enters the diner (similar to Episode 2) and stops the other Max from messing with the real Max's head. Max is then taken to a trip of all the memories she had with Chloe together. At the end of it, Max exits the nightmare and both Chloe and Max see the storm edging closer to the town. Max assumes her rewind power being discovered after the incident in the bathroom as the reason for the storm. Chloe then gives Max the blue butterfly photo she took in Episode 1, making Max choose the final decision: Sacrifice Chloe to save Arcadia Bay or sacrifice Arcadia Bay for Chloe.

If Arcadia Bay is sacrificed, Max tears up the butterfly photo. Max and Chloe are seen driving out of the ghost town in the ending scene.

If Chloe is sacrificed, Max is brought all the way back to the bathroom where Nathan first shot Chloe. Max, feeling helpless, crouches behind the stalls and cries as she hears the gun shot. After some time, Arcadia Bay is seen bathing in sunlight again, while Joyce, David, Warren, Max, Kate, Victoria, Dana, Justin, Trevor and Principal Wells mourn over Chloe at the cemetery. Frank and Pompidou is seen overlooking the ceremony at a distance as the blue butterfly flies over them and lands on the coffin. Max looks at it and smiles, remembering what it signifies and how it all started.

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