The movie is set in 1970s Berlin during the German Autumn. The real-life events (the hijacking of an airplane by the PLAF and imprisonment of members of the RAF are reported on in the background).
A teenaged girl named Patricia (Chloë Grace Moretz) runs through the streets of Berlin to her psychologist's office. She is met by her psychologist, an old man named Josef Klemperer (Tilda Swinton, credited as Lutz Ebersdorf). Patricia claims that the instructors at her dance academy are witches and have been trying to take her body. Dr. Klemperer is clearly skeptical. Patricia then runs out of the office, leaving a bag of her belongings behind.
Meanwhile, American dancer Susie Bannion (Dakota Johnson) gets off of a train in Berlin. She walks to the dance academy and says that she has been invited by famous dancer Madame Blanc (Tilda Swinton) to audition. She begins auditioning before two of the other instructors and, from several rooms away, Madame Blanc senses Susie's presence. Madame Blanc appears to teleport into the audition room to watch Susie. As Patricia has "left" the academy, they decide to admit Susie into their program.
Later that night, the instructors meet. It turns out that they are, in fact, a coven of witches. The witches hold a vote on whether to replace their leader Mother Markos (Tilda Swinton again) with Madame Blanc. Mother Markos is not in attendance, and its mentioned that her body is ravaged by disease. The majority votes for Mother Markos to maintain her leadership even though her plans led to the loss of Patricia. The witches note that Mother Markos has ordered them to try to complete the ritual they had been conducting on Patricia with another student.
Susie meets fellow dancer Sara (Mia Goth) who helps her move into the Academy. Susie learns that the dance academy has been open for ages, even throughout World War II, and all the students get free room and board. Susie displays immense raw talent and also, appears to intuitively respond to the powers of the witches.
The instructors introduce Susie to the other girls and claim that Patricia left them to join the revolutionaries (like the RAF). A dancer named Olga (Elena Fokina) breaks down and says that the instructors are lying. As Olga leaves the academy, Madame Blanc asks Susie to dance a part and casts a spell on Susie that causes her dance moves to injure Olga who has been trapped in a secret room. By the end of the dance, Olga's limbs are completely splintered and contorted, and Olga is barely alive. The other witches impale Olga with meat hooks and drag her down a secret passageway.
During one practice, Susie begins dancing while Mother Markos is hidden below the dance floor (all we see is Markos' clawed hand beneath the dance floor). Markos deems Susie a perfect vessel for her to switch bodies with and orders Madame Blanc to begin preparing Susie for a ritual to take Susie's body for herself.
Meanwhile, Dr. Klemperer begins reading Patricia's diary that was left in his office. He learns more about Patricia's theories that the instructors are part of a coven. All witches work in service of three ancient witches - Mother Lachrymarum, Mother Tenebrarum, and Mother Suspiriorum. According to Patricia, Mother Markos believes that she is Mother Suspirorum and she seeks a new body to maintain eternal life. Though Dr. Klemperer thinks Patricia's witch talk is pure superstition, he theorizes that the instructors are part of a dissident group. He calls the police and reports that Patricia has gone missing. The police go to the dance school but are put under a spell by the witches where they hallucinate seeing nothing suspicious at the school (in reality, they were put into a coma, and the witches strip them naked and mock the men's genitals). Shortly thereafter, we learn that Dr. Klemperer's wife (intimated to be a Jew) disappeared during World War II, and Dr. Klemperer has long wondered about her fate.
Sara and Susie begin investigating Patricia's disappearance, learning that the instructors have eliminated all trace of Patricia (and Olga) having ever attended the school. Sara and Susie also grow closer, with Sara comforting Susie when Susie has nightmares that are given to her by the coven.
At the same time, Madame Blanc begins bonding with Susie. She learns that Susie was raised in an Amish household and disobeyed her family by attending Madame Blanc's dance recitals when she toured the US. Susie's mom is dying, and Susie's mom tells the local clergy that her only regret in life is giving birth to Susie. Madame Blanc gives Susie private lessons, teaching her to overcome her dance limitations (and possibly transferring skills from other dancers into Susie). Madame Blanc and her supporters also grow more wary of performing the ritual demanded by Mother Markos.
Dr. Klemperer approaches Sara and warns her that she is living with dangerous people (and confides in Sara about Patricia's suspicions that the instructors are witches). Though Sara initially refuses to listen to Dr. Klemperer, she eventually begins digging deeper. One night, she finds a hidden passage. She follows it down to a room filled with ancient relics and steals one of the witches meat hooks. She also witnesses the coven engaged in a ritual before fleeing back to her room. The next day, Sara visits Dr. Klemperer and tells him that all of Patricia's suspicions were correct and she gives him the meat hook she stole. The witches become aware of Sara's actions and also decide to punish Dr. Klemperer for his interference by making him a witness to their ritual to transfer Mother Markos into Susie's body (stating that the horrors of the ritual will drive him mad).
The students prepare to put on a recital that appears to double as a pre-transfer ritual. Susie, of course, is the lead dancer. The night prior to the performance, Madame Blanc appears in Susie's room, and the pair has a telepathic conversation wherein Susie deduces that Madame Blanc loves her (like a mother). One of the supporters of Madame Blanc commits suicide in guilt and/or fear of what they are about to do to Susie.
The night of the performance arrives, and Sara decides to search the catacombs beneath the school while everyone else is at the recital. Dr. Klemperer attends the recital. In the catacombs, Sara finds Patricia alive but in a withered condition (as though the witches have been stealing her life force). Sara also finds Olga having been driven mad and her limbs missing. As Sara flees, she steps into a hole conjured by the witches, and her shin is shattered (the bone literally sticking out of her skin). Some of the witches come for Sara, heal her leg, and put her in a trance so that she goes back into the recital. As the climax of the performance nears, Madame Blanc is told that the transfer will take place that night. At the climax, Sara's shin splinters again and the crowd runs out of the school in a panic. Dr. Klemperer is particularly disturbed as he saw that Sara's eyes had changed color and he finally believes that the instructors are witches.
The girls (except Sara, who is whisked away) all go out with the instructors to celebrate the recital. All the dancers but Susie are put into a trance. Meanwhile, now fearing the actual power of the witches, Dr. Klemperer tosses the meat hook and all of Patricia's belongings into the river (trying to cut all ties with the situation). He turns around to find his wife Anke (Jessica Harper - who played Susie in the original movie Suspiria) standing there. Anke explains that she eventually fled Germany and through a series of circumstances, ended up in England where she remained ever since. The pair embrace and Anke slowly leads Dr. Klemperer to the school where we discover that Anke was an illusion. He is captured by the witches who chastise him for not doing more to help his wife when he had the chance and for throwing their meat hook in the river. They strip him and take him down to the catacombs where he will witness their ritual.
That night, Susie awakens and follows a spectral light into the catacombs. She arrives to find her entranced peers dancing wildly, Dr. Klemperer weeping in the corner, the instructors in robes, and the hideous Mother Markos awaiting her arrival. Mother Markos is hideous, covered with tumors and boils. Susie descends the steps, saying she is prepared to sacrifice her life... for Madame Blanc. Madame Blanc cries out to Susie that she does not have to do this and that something "feels wrong." Mother Markos lashes out at Madame Blanc and severs Blanc's spine and neck. As part of the ritual, Sara is disemboweled while still alive. Mother Markos then demands that Susie kill her own mother (and casts a spell allowing Susie to do so) in order to complete the ritual. While contemplating Mother Markos' requests, Susie asks which of the ancient witches Mother Markos serves. Markos claims she serves Mother Suspiriorum. Susie smiles and reveals that, in fact, she is Mother Suspiriorum and strikes Mother Markos dead (likely for perverting the coven, abusing her power, and falsely claiming to be Mother Suspiriorum).
Susie then summons forth the embodiment of Death. Death approaches each witch that supported Mother Markos over Madame Blanc and kills them (the head of each witch explodes when touched). Susie then approaches Patricia, Olga, and Sara and asks what she can do for those sweet girls. They all ask to die, and Susie kills them all in a gentle manner. Dr. Klemperer is then released, and the remaining witches are ordered to clean up the mess they have made.
The next day arrives, and everyone acts as though nothing ever happened (the students appear to have had their memories of the prior night's events wiped away). An announcement is made that Madame Blanc will no longer be able to teach at the school (and although Madame Blanc's neck and spine are severed, she still appears to be alive). The remaining witches are clearly in service to Susie/Mother Suspiriorum.
That night, Susie appears in Dr. Klemperer's bedroom where he is bedridden. She apologizes for the acts of her witches, stating that their beliefs had been perverted and Susie needed to gather the strength necessary to stop them. In a show of good faith, Susie tells Dr. Klemperer of Anke's fate. While Anke did try to escape Germany, she was apprehended and sent to a concentration camp. There, Anke died from exposure when the commandant forced all the prisoners to stand outside in the freezing cold while a "census" was being taken. Despite Anke dying, Susie lets Dr. Klemperer know that she was surrounded by prisoners who cared for her and that her last memory was of her first date with Dr. Klemperer and of his love for her. Susie explains that while many people must feel guilt and shame for their actions, Dr. Klemperer is not one of them. She then erases all of his memories pertaining to the dance school and those who resided there.
After the credits we observe Susie/Mother Suspiriorum staring at something off-camera and breaking into a smile.
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