The story begins with Dr. Kathy Grieff (Jennifer Jason Leigh) entering a secure area for a meeting with Morgan (Anya Taylor-Joy). The unsettling encounter is monitored through surveillance cameras as they share a meal together. Kathy, expressing her frustrations, reveals her inability to permit Morgan to go outside. In a dramatic turn, Morgan abruptly tosses the table's contents aside, leaps over it, and violently attacks Kathy, stabbing her in the eye. This prompts the intervention of two other doctors who quickly sedate Morgan.
Following this chaotic incident, Lee Weathers (Kate Mara), a risk management consultant, arrives at the facility to assess the situation. She meets Amy Menser (Rose Leslie), Morgan's behaviorist, and Skip Vronsky (Boyd Holbrook), the nutritionist on the team. Later, Lee converses with Dr. Simon Ziegler (Toby Jones), who elucidates the complex and rapid development of Morgan, an artificial life form designed to mature quickly over six months. They share a shocking video showcasing Morgan's emotional capacity, a trait she developed while spending time with Amy, whom she views as a sister.
In a private meeting, Lee finds Kathy in a vulnerable state, heavily medicated and bandaged. Kathy expresses remorse for provoking Morgan into attacking her, reminiscing about how joyful Morgan once was before being confined again. When Kathy refers to Morgan using female pronouns, Lee insists on referring to her as "it."
Later, Lee visits Morgan, who has already shown an awareness of her presence. Despite appearing friendly, Morgan’s intelligence is evident, but Lee is far from impressed, which is apparent to Ziegler. That evening, Lee dines with colleagues, including Drs. Darren and Brenda Finch (Chris Sullivan and Vinette Robinson), Ted Brenner (Michael Yare), and Dr. Lui Cheng (Michelle Yeoh), whom Morgan considers her maternal figure. Amidst the dinner, Lee and Skip share a moment, revealing a past romance between Skip and Amy, which ends awkwardly when Skip kisses Lee but quickly apologizes.
A poignant flashback shows Amy taking Morgan outside to breathe in the fresh air, where they encounter a deer in distress. In an act of mercy, Morgan breaks its neck. The following day, Dr. Alan Shapiro (Paul Giamatti) conducts Morgan's psychological evaluation but quickly spirals into a heated confrontation, leading Morgan to retaliate violently. When she escapes, Lee pursues her with a tranquilizer.
In a chilling turn of events, Morgan finds herself strapped to a table, begging the doctors not to proceed with her termination. Yet, Dr. Cheng coldly denies any maternal connection, and as Morgan is sedated, turmoil ensues. Lee's determination leads her into confrontation, where she is nearly overwhelmed by Ted but regains control through sheer willpower. The boundaries of safety are breached, resulting in tragedy as Morgan retaliates against those who've wronged her, leading to the swift and brutal downfall of the staff: Ted, Kathy, Dr. Ziegler, and others fall victim to her wrath.
After a harrowing sequence of events, Morgan and Amy attempt to escape the chaos. Lee, fueled by determination, follows and attempts to save Amy while confronting Morgan once again. In a battle of resilience, Lee eventually triumphed in the depths of the woods, but not without incident, suffering injuries herself.
As the story closes, the aftermath of destruction haunts the facility. Jim Bryce (Brian Cox), head of the company overseeing the Morgan project, proclaims it a failure, but the chilling last image reveals Lee staring at her own hands, mirroring Morgan's earlier act of self-examination. The lingering question remains—what does this connection mean for her future?
