The season 2 premiere of "School Spirits" kicks off with Maddie confronting Mr. Martin, demanding answers about her untimely fate. Meanwhile, Charley, Rhonda, and Wally strive to reach Maddie, their urgency palpable. However, Mr. Martin remains evasive, dashing off just as Maddie's questions intensify. He halts momentarily to caution Maddie against probing further, his voice tinged with regret for ever initiating their tumultuous ordeal. Concurrently, Charley, Rhonda, and Wally manage to extricate themselves from the basement, only to discover Mr. Martin's absence upon reaching Maddie.
Elsewhere, Simon pedals away on his bike, determined to escape the spectral haunting of Maddie. Convinced of his impending sanity's collapse, he seeks solace in severing ties with Maddie's spectral presence.
In a separate narrative thread, Janet boards a bus bound out of town, still encased within Maddie's flesh. Haunted by recent events, her thoughts drift to a harrowing flashback—her final, contentious exchange with Mr. Martin before her soul became ensnared in Maddie's body. Alighting at a secluded stop, she purchases a map from a local convenience store, her demeanor stirring concern in the cashier who offers, albeit unsuccessfully, to assist her.
Meanwhile, Claire and Nicole keep vigil at Xavier's hospital bedside, his condition critical. Torn between seeking justice and granting Maddie the benefit of the doubt, Nicole leans towards patience, suggesting they await Xavier's recovery. However, doubts linger; could Maddie be seeking vengeance, with Nicole potentially next in her sights? Despite these fears, they concur to wait.
Back at the school, Maddie unburdens herself to the other spirits, sharing fragments of her final day. Anger simmers towards Mr. Martin; the quest for answers grows more desperate with his disappearance. They ponder his strange hobby of amassing memorabilia linked to their deaths and his clandestine note-taking. A desperate search for Mr. Martin ensues, Rhonda's patience wearing thin.
Wally's frustration peaks as he finds the hatch exit, or fallout shelter door, resistant to his efforts. The lock mechanism refuses to reset, exacerbating tensions. Accusations fly, with Rhonda accused of betraying them by allying with Mr. Martin in the past. They realize the necessity of a living soul to access the shelter, and Simon emerges as their sole viable option.The following day at school, Simon deliberately ignores Maddie and requests the teacher to reassign him to different classes. He meticulously selects spots where no fatalities have occurred, ensuring Maddie cannot reach him. Maddie strives valiantly to reconnect with him, but each attempt falls flat. Meanwhile, Wally is tormented by doubts regarding Maddie's true fate. Though relieved that she still harbors hope, he senses a profound shift in their world since her arrival. He unearths the school map and persists in his search for Mr. Martin.
In the hospital, Xavier's condition stabilizes, albeit precariously. Claire finds herself in hot water with her parents concerning the Xavier saga. The sheriff, Xavier's father, visits and informs them that the police are actively pursuing Xavier's assailant.
Subsequently, Claire dials a payphone to inquire at the bus station if a girl matching Maddie's description boarded a bus. The station confirms that Maddie disembarked in a town called Birmingham. Concurrently, Nicole attempts to reach Simon, increasingly frustrated by his silence to her calls and messages.
Back at school, Rhonda's patience with the marching band snapped like a twig, prompting her to snap at them, urging them to rouse themselves from their slumber. Maddie, ever the peacemaker, stepped in to soothe her frayed nerves, reassuring her that the blame did not rest solely on her shoulders. Yet, Rhonda's frustration spilled over, confessing her envy towards Maddie. Struggling to let people in, she felt an acute loneliness upon witnessing the burgeoning closeness between Wally and Maddie. She further unveiled that, on the fateful night of the party, she had glimpsed Mr. Martin with her Berkeley acceptance letter. Desperate for answers that would propel her forward, she had betrayed Maddie and Simon's secret communication in exchange for it. Maddie, comprehending the depth of Rhonda's turmoil, forged a pact with her to eschew secrets henceforth.
As the trio ventured further into their quest to find Mr. Martin, they delved into his diaries, which painted a hurtful portrayal of Charley. Meanwhile, Wally unmasked Mr. Martin's macabre hobby: a death map meticulously charting every fatality within the school's confines. Maddie realized she could confront Simon at the greenhouse, reaching out to him with poignant reminders of their shared pain during her father's funeral. Simon listened intently but steadfastly denied any significance to their connection.
Elsewhere, Janet journeyed to her decrepit former abode, untouched by human hands for years. The neglected house served as a poignant reminder of her grandmother's unwavering support for her scientific aspirations and college dreams. Driven by nostalgia, she ventured to the family burial ground and, with trembling hands, disinterred her grandmother's grave.
As dusk descended, Simon returned to school, his resolve hardened against the notion of Maddie being a figment of his imagination, strengthened by her misremembering of her father's funeral. He agreed to aid in opening the fallout shelter, revealing Mr. Martin's grim secret: Janet, imprisoned there for months. The episode concludes with Janet, lying on her grandmother's grave, tears streaming down her face, while Xavier, confined to a hospital bed and immersed in coding, began to see spectral visions haunting his every glance.