In Dreamcatchers, Hayden was in Ken Yukimura's sophomore-level history class at school when she noticed Tracy Stewart, a senior, sitting next to her, anxiously clenching the desktop to the point of snapping it in half. Upon seeing that she's in her pajamas and that her bare feet are covered in dirt, she questioned Tracy's presence in the class, but Tracy was in a trance and unable to reply. Unbeknownst to Hayden, her classmate Liam Dunbar had left to alert his friend and Alpha Scott McCall for assistance before pulling the fire alarm to get the rest of the class out of the room.
When Hayden tried to get Tracy to leave the classroom with her, believing that they were having a fire drill, Tracy grabbed Hayden roughly by the wrist with her clawed hand and began squeezing it so hard that her wrist began bleeding. Scott soon arrived and began quietly trying to calm Tracy down enough to let go of Hayden, who whimpered that she was hurting her. Tracy, who was hallucinating that the Dread Doctors were there as a result of being in the midst of a night terror, finally let go of her and informed Hayden, Liam, Scott, and Mr. Yukimura that the Dread Doctors were coming for all of them before falling unconscious, a puddle of the Modified Mercury that the Dread Doctors injected into her upon her transformation into a Chimera pooling out of her mouth.
Hayden then watched as Scott picked up the unconscious Tracy and joined his Beta Malia Tate and best friend Stiles Stilinski in leaving the school. Still clutching her wounded wrist, Hayden asked Liam where Scott and the others were taking Tracy, and Liam, knowing that they were going to the Druid Alan Deaton's animal clinic, lied and stated that they were taking Tracy to the hospital. He then asked Hayden if she needed help getting to the nurse's office, but Hayden sarcastically retorted that she would manage it before rushing away to the girls restroom to clean up. After running her bloody wrist under the water, Hayden was stunned speechless when she realized that her claw wounds had already miraculously healed.
In Required Reading, Liam, at Scott's request, was keeping an eye out for anyone who seemed to be exhibiting signs or symptoms of being a newly-turned Chimera while also trying to get back into Hayden's good graces after spilling $200 worth of drinks while she was working at Sinema several days earlier. After meeting her at the club to give her back some more money he had earned, the two began talking about the mycophenolate that she had to take to prevent her body from rejecting the donor kidney she received in a transplant several years earlier.
When she made a comment about her boss, Phil, docking her pay because he knew that since she was underage and working under the table, there was nothing she could do to stop him, she remarked that Liam should listen to what Phil was saying to a potential new hire to prove her point. However, when Liam had to use his Werewolf hearing to pick up on the conversation, he realized that Hayden was one of the Chimeras that Scott warned him to look out for. He then used a glowstick to confirm his suspicions, as the light caused a flare off of her eyes.
In Strange Frequencies, Liam, intending to tell Hayden the truth about the supernatural before bringing her to the pack for further help, explained the current situation regarding the Dread Doctors and the Chimeras. However, Hayden did not believe Liam and told him to get away from her, which led him to partially-shift and roar in her face to prove it to her. Unfortunately for him, Hayden simply screamed and punched him in the face before driving off, only for her car to be stopped by the Dread Doctors using their electromagnetokinetic powers so that they could capture her. Just before they reached the car, Liam appeared, having jumped on the top of her car and pulled off the moon roof before pulling Hayden out so they could run away.
Liam then brought Hayden to the McCall House, where Hayden abruptly ran into the bathroom attached to Scott's bathroom and locked herself inside. When Scott and Stiles returned from Beacon Hills Animal Clinic, Scott attempted to coax Hayden out, assuring her that she didn't have to believe them about the supernatural, but that he needed her to open the door or he would have to break in himself to make sure she was okay. Before he could do the latter, Hayden unlocked the door, allowing Scott, Stiles and Liam inside; upon opening the door, the three were stunned to find Hayden with the glowing golden eyes, fangs, and claws of a Werewolf, confirming once and for all that she was, in fact, a part-Werewolf Chimera as Hayden replied, "I believe you."
The next morning, the McCall Pack and their allies convened to come up with a plan to protect Hayden from the Dread Doctors, which involved Hayden lying to her older sister and guardian, Deputy Valerie Clark, and saying that she was staying the night with a friend. Scott and Stiles then decided their best course of action was attempting to use the convergences of Telluric Currents running throughout Beacon Hills against the Dread Doctors, as they were unable to enter Eichen House as a result of a powerful convergence running under it until Kira Yukimura's Kitsune foxfire disabled them. Since the next strongest convergence was at Beacon Hills High School, they determined that it would be the best place to create a fortress against the Doctors, especially with the help of Jordan Parrish's modified frequency disrupters.
That evening, the plan was put into motion, with Parrish patrolling the outside perimeter, Malia Tate patrolling the entrance hall to the school, and Scott, Lydia Martin, and Liam in the locker room with Hayden to protect her in person. When Scott overheard Liam, who was clearly beginning to develop romantic feelings for Hayden, reassuring her that she would learn to control her powers and that she was still herself, Scott became nostalgic, both regarding his past relationship with Allison Argent and current relationship with Kira.
A short time later, Liam noticed a duffle bag full of chains and restraints and asked Scott about it, forcing Scott to admit that he wanted to try to capture a Dread Doctor if the opportunity presented itself. Liam correctly deduced that this meant Hayden was the bait, which angered Liam and caused Hayden to become afraid. Scott, overwhelmed by the task at hand, became frustrated and argued that people were dying and that they knew virtually nothing about the threat the Dread Doctors posed to them, nor did they know anything about the Doctors' plans for Beacon Hills. When Scott stated that someone had to protect everyone, which meant that someone needed to be the bait, Hayden and Liam began to understand his position. However, Liam forced Scott to promise that he would do whatever he had to do to protect Hayden, and Scott agreed to do so without question.
Just then, Hayden remembered that she forgot her anti-rejection medication and stated that she had an extra bottle in her locker, but when she offered to go get it herself, Scott, remembering his promise, asked her what her locker number and combination was so he could get it for her. Unfortunately, the Dread Doctors then used their powers to cause Parrish, Malia, Scott, and Lydia terrifying hallucinations that incapacitated them, allowing the Dread Doctors to easily capture Hayden and Liam. After Mason Hewitt arrived and snapped Scott out of his hallucination by slicing his hand open with a scalpel, Scott and the others realized to their horror that Hayden and Liam had been taken. Meanwhile, Liam awoke in the Dread Doctors Operating Theater to find that he was on the floor, hooked up to a large, painful intravenous drip of Wolfsbane in his arm while Hayden was being operated on by the Dread Doctors.
In Ouroboros, Scott stayed up the entire night, running across Beacon Hills and through the nature preserve with Malia in an effort to locate Hayden and Liam, but Scott got no response to his Alpha Roars. When this failed, they returned to the McCall House, where Lydia, Stiles, and Theo were waiting for them. Scott ignored their questions and made his way upstairs to his bedroom, where Mason was reassuring the newly-discovered Chimera, Corey Bryant on how slowly he was reading The Dread Doctors novel, as they were trying to get him to remember anything about his transformation into a Chimera in hopes that he could give them details about the Dread Doctors' lair.
In an uncharacteristically impulsive move, Scott insisted that reading the book would take them too long and quickly stabbed the back of Corey's neck with his claws to perform the Memory Manipulation Ritual to speed up the process without Corey's consent. Since Corey's memories were blurry as a result of them being repressed by the Dread Doctors' own memory manipulation powers, Scott was only able to make out that their operating theater was located in the tunnels underneath the Water Treatment Plant. He then recruited Malia to come search the tunnels with him due to her Werecoyote superhuman sense of smell, though Mason, as Liam's best friend, refused to stay behind and instead joined them in their search.
While in the tunnels, Scott, Malia, and Mason had no luck in finding where Hayden and Liam were located, and Scott became so desperate that he began to have an asthma attack. This only increased Scott's self-loathing regarding Hayden and Liam's capture, as he perceived it as yet another weakness and refused to use his inhaler until Malia and Mason forced him to do so. After running out of luck in finding Hayden and Liam, Scott, Malia, and Mason returned home to find that Theo had located them and rescued them from the Dread Doctors' holding cell. Relieved to see the two sleeping on the couch, Scott gave Theo a grateful look as he hugged him, though it was clear that he still felt badly about the fact that he wasn't able to complete the mission himself.
In Lies of Omission, after Scott and Theo found Corey Bryant killed by the Dread Doctors after rejecting his transformation and vomiting up Modified Mercury, the two realized that the Doctors would be going after Hayden next and tracked her and Liam to Sinema, where Hayden had stopped by to pick up her paycheck to give them money to flee Beacon Hills until the threat was over. By the time Scott and Theo arrived at the club, the Dread Doctors were already there and fighting Liam, leading them to join the fight in order to buy Hayden and Liam enough time to flee. Unfortunately for them, Hayden was cornered by The Geneticist in the back hallway of Sinema, where the Doctor injected Hayden with an overdose of Modified Mercury as a result of her failed transformation.
Horrified, Scott instructed Theo to take Hayden and Liam back to the animal clinic and assured them that he would meet them there. After Scott finally made it inside following a big fight between himself and Stiles as a result of the revelation that Stiles had killed Donovan Donati, Liam reminded Scott of his promise to protect Hayden at all costs and begged him to give her the Bite, to which Scott sighed and said "No."
In Status Asthmaticus, Liam reiterated Scott's promise, but Scott argued that he was saying "no" because of his promise-- between the fact that Hayden was weakened to near-death and had the mysterious Modified Mercury compound in her system, the Bite would be more likely to kill her than it would be successful in saving her life. Liam took this to mean that Scott didn't want to save her, but Scott insisted that they would save Hayden another way. When Theo, who was watching over Hayden as she gradually got weaker, argued that they needed to come up with a solution quickly, Scott decided to bring in his mother, Melissa, to use chelation therapy to try to remove the mercury from her blood and save her with science rather than the supernatural.
After hooking Hayden up to the chelation solution, Hayden weakly informed them all that she didn't want to die without her sister Valerie there with her, and Scott offered to go find her himself and bring her back. After being told that Valerie would be at the high school, dealing with the fact that something, Scott went there in hopes of finding her, only to be sidetracked by a text message from "Lydia" telling him to meet her in the library. It was there that he found her cell phone sitting on a bookshelf and realized that he had been led into a trap just as he caught Theo completing a Mountain Ash barrier around the building.
When Scott remarked this wasn't possible, Theo revealed that he was, in fact, a Werewolf-Werecoyote Chimera, which was how he was able to handle Mountain Ash, before stating that he would be unable to leave or call for help due to the cell signal disruptors he stole from Jordan Parrish, preventing Scott from finding Valerie and bringing her back to Hayden. That evening, after Scott attempted to escape from the school by jumping off the roof and had realized that the return of his asthma was due to Theo lacing his inhaler with purple wolfsbane, he was confronted by Liam, whose anger had already been enhanced by the supermoon overhead and manipulated by Theo.
Liam accused Scott of lying to him about his promise to save Hayden, to which Scott argued that the Bite wouldn't have saved her and that Theo wanted Liam to kill him because he couldn't steal a True Alpha's power on his own-- he needed his bitten Beta to do it for him so he could then kill Liam and steal his power himself. Liam argued that his desire to kill Scott was real and wasn't coming from Theo, and that if he had to do so to get the power to give Hayden the Bite himself, then he would do so. The two then got into a vicious, knock-down, drag-out fight in the library, where Liam would have killed Scott had Mason, his best friend who was somewhat of an anchor for him, not interrupted to inform him that Hayden had died.
Theo, who was furious that his plan had failed, took his frustration out on Mason by knocking him out before Scott baited him into putting him out of his misery by killing him himself, though Scott's mother, Melissa, was ultimately able to use the power of the supermoon and CPR to bring him back to life despite the fact that he had been dead for nearly twenty minutes. Afterward, Scott lamented the fact that he had lost his entire pack, implying that Hayden's death was one of many major mistakes he had made in the past weeks. Meanwhile, unbeknownst to Scott, Liam, and the rest of the McCall Pack, Theo was at the Nemeton, where he used the Dread Doctors' Green Serum to resurrect Hayden, Corey Bryant, Tracy Stewart, and Josh Diaz before declaring that they were now his pack.
In The Last Chimera,
In Damnatio Memoriae,
In The Sword and the Spirit,
In Lie Ability,
In A Credible Threat,
In The Beast of Beacon Hills,
In Apotheosis, Hayden gets hurt by Sebastien as she tried to kill him with Tracy's Kanima venom. Scott gives her the bite to save her and she become a real werewolf and Scott's second bitten Beta.