The Orville is flying through a storm, sustaining some damage. Kitan is called upon to help move a bulkhead off a pinned crew member and is momentarily paralyzed when faced with a fire. By the time she comes around and makes her way to the crew member, he is dead.
The crew holds a memorial for Lt. Harrison Payne with Chief Engineer Newton delivering the eulogy. Kitan feels guilty and hits the gym in the simulation deck to work out her emotions, destroying a heavy bag in the process. Commander Grayson and Dr. Finn come to see her and explain that it wasn't her fault. Kitan doesn't buy it and insists on resuming the program despite the fact Malloy, LaMarr, and Bortus have apparently reserved the simulator for a French Revolution pistol duel in the time slot after her.
Mercer is having some difficulty writing a condolence letter when Kitan comes to his ready room to resign her position. He refuses to accept her resignation and insists that she speak to someone about her fear of fire. Kitan speaks to her parents who want her to return to Xelaya and quit the military. When she asks them about fire, her mother recounts an incident from when she was a baby and a fire broke out in the house.
As Kitan heads down the hall, she sees a clown who runs at her, bumps past her, and then disappears around a corner. She goes to the captain and demands he relieve her of duty because she's obviously going crazy. LaMarr doesn't like clowns. Checking the video surveillance, they find the clown on the footage but then he still disappears. Isaac confirms he was an unidentified human and that the internal scanners cannot detect him now.
Mercer sends the staff to find the intruder. They conduct a deck by deck search. Kitan and Bortus are paired but the lights in the shuttle bay aren't working. Kitan is attacked by the clown and he repeatedly seems to disappear and reappear to attack again until she finally shoots him and he disintegrates.
The crew is placed on yellow alert to be on the lookout for clowns. Kitan and Grayson make plans to meet for a drink but when Grayson goes to her quarters, there is nothing but an abyss through her doorway. Kitan saves her and they report to Mercer who hypothesizes that there's something going on with their perceptions.
They go to Dr. Finn and she is reasoning out what has been seen and experienced when Bortus enters and announces that there is an alligator in the cargo bay that he crushed it with a chair. Dr. Finn agrees to conduct a brain scan on each of them. Kitan is being examined when she notices that Dr. Finn's staff is missing and she finds that strange. Dr. Finn restrains Kitan for the brain scan which feels suspicious, especially when she is unable to break free.
Nurse Park enters when Dr. Finn is out of the room. Kitan asks him to release her but he is unable to do so because the code has been changed. Dr. Finn returns and shoots him in the back. Dr. Finn indicates that she is about to operate on her. Kitan manages to break one hand free, pick Dr. Finn up and fling her across the room, knocking her unconscious.
Dr. Finn is placed in the brig and Mercer questions her to no real result. She indicates that something scary is coming for them all.
In a meeting of the senior staff, Grayson hypothesizes the storm they encountered somehow crossed a divide between reality and thought. Bortus notices a tarantula on the table. Suddenly the room is infested with them, crawling down the wall in a curtain. One lands on Malloy's face and he screams and runs out of the room. The rest follow, Mercer grabs a weapon and returns to the room where all the spiders have disappeared.
Mercer orders the ship back into the plasma storm in an attempt to figure out what has happened to the ship. Kitan and Malloy head down a corridor and are confronted and chased by a giant alien spider which catches Malloy and eats him. Kitan pursues it and it disappears.
Kitan returns to the bridge to find it abandoned and the ship about to re-enter the plasma storm. She is unable to contact anyone else on board. She searches various decks and areas for others but doesn't find anyone until she reaches Engineering and finds Isaac. He explains that he found himself alone on the bridge and came down to Engineering looking for answers. As they try to piece together what has happened, Kitan comes to suspect Isaac and confronts him. He attacks her and they fight. She manages to subdue him and runs out of Engineering and arms herself. Isaac approaches her again and she shoots him and the ship's computer reports that the inner hull has been compromised and she needs to evacuate. Kitan runs down the corridor and it is revealed that she is in the simulation suite. Mercer, Grayson, Isaac, and Dr. Finn watch from an observation room and Dr. Finn insists that they shut down the program.
Isaac informs them that they are unable to shut down the program and Kitan must complete the program in order for her to get out of the simulation suite.
Back in the simulation, Kitan is trying to evacuate aboard a shuttle when she is attacked by Isaac again and he sets a fire in front of her to try to prevent her from escaping the shuttle bay. She faces her fear and flies through the fire. From a distance, she watches the ship explode. The simulation ends and she finds herself in the empty simulation suite. Mercer, Grayson, Dr. Finn, and Isaac some in to explain she completed the simulation and she is shocked.
Debriefing in the captain's ready room, they explain that it was her idea to create a simulation to test her against various fear-inducing situations in a simulation created by Isaac and have a memory wipe to make her think it was real. Locking the system was not an approved part of the plan and she apologizes. Everyone commends her on her success and points out that she should have no insecurities about doing her job from this point onwards.
She goes to bed and sleeps well.