The night of the winter formal, Lydia is attacked by Peter Hale and rushed to the hospital. Melissa watches over her over the weekend. She's outside in the hall with Lydia's dad and Stiles while Lydia takes a shower and comes rushing in when she hears her scream. Lydia is missing, and the window is open.
The next student of Beacon Hills High School that she treats is Erica Reyes. Erica has epilepsy, and she has a seizure while trying to climb the rock wall in the gym. Melissa treats her in the ER but leaves before Derek appears.
A couple of days later, Victoria Argent comes into the ER with a deep knife cut on her arm. She takes the opportunity to ask Melissa about Scott and Allison. They had assumed their kids were no longer dating. Melissa admits that Scott isn't as heartbroken as she would have expected.
Now that Scott plays lacrosse regularly, Melissa makes an effort to attend his games. She notices Matt Daehler taking photos at one of the games and asks if he's the yearbook photographer. He tells her that he just likes taking photos of things that interest him.
The day after Danny Mahealani was attacked at the Jungle, Melissa stops Scott in the hospital hallway to talk to him about his grades. She's concerned that if he fails he's going to be held back a grade. She tells Scott that he can't fail, which he knows better than she can imagine.
When Scott and Stiles get caught having kidnapped Jackson, Melissa has to go down to the sheriff station. She stands in the interrogation room and listens as the restraining order is read against them. She's beside herself with what to do about all the changes in Scott lately. She counts off his bizarre behavior and the late nights coming home and having to beg Mr. Harris to let him make up a Chemistry test, and then tells him that he's grounded. He gets no TV (which is already broken) and no Stiles. Stiles starts to protest, but Melissa yells, and he backs off. She also takes Scott's car keys. She fumbles with trying to remove the key from the keyring, and Scott eventually just puts his hands on hers to make her calm down.
She asks him what's going on with him and whether it's about Allison. Scott sighs and asks her if she really wants to know. Melissa asks if it's about Scott's dad, and decides it must be that and they'll talk about it at home.
While Scott is at school, Melissa decides to snoop around his room. She decides to "straighten up" and puts his guitar back against the wall. She checks his chair, his books, and his closet. Then under his mattress and digs through his clothes hamper. She checks his desk drawers, and then while sitting at his desk sees a box of condoms. There's only one left from a box of 12. She looks distraught.
She goes to talk to Victoria, who now works in the principal's office at the school. Victoria tells Melissa that she thought their kids were no longer dating. "Me too. But it looks like they are. And more. A lot more." Victoria asks how Melissa knows it's not some other girl were severely low standards. Melissa replies that Allison is the only girl Scott has ever talked about. Melissa says she wants them to be safe. Victoria agrees.
A few days later, Scott calls her while she's at work and asks if she remembers a teenager going to see Jessica. She tells him that she talks to a lot of people, so he sends her Matt's yearbook photo. She says that she remembers Matt because he was tracking mud in the hall. Scott asks his mom to come to the sheriff's station so she can make a statement.
Melissa comes into the station to find Matt holding a gun on Scott. Scott tells his mom to do what Matt says because he promised he wouldn't hurt her. Matt confirms and then shoot Scott. Melissa screams. Matt orders Melissa back, and Scott begs her to comply. Matt locks Melissa in a cell in the same room with Sheriff Stilinski. She thinks Scott is going to bleed to death.
Sheriff Stilinski manages to rip the ring that he's cuffed to off the wall at last, while Stiles, who has been paralyzed by the kanima, struggles to crawl into the room with them. Matt runs up to the Sheriff and punches him, knocking him out. Melissa begs Matt to let her see Scott, and Matt yells at her for being clueless. Derek appears in one doorway, growling and eyes glowing. The kanima appears in another.
Derek and the kanima fight, while Melissa watches. Derek tries to keep the kanima away using a chair, but the kanima throws him hard into a wall. Then it crawls on the bars in front of Melissa. While it's paying attention to her, Scott shoves his claws into its back. Melissa asks Scott if he's okay, and he turns to look at her while he's still wolfed out. She starts to cry and backs away from him. Rather than try to explain, Scott leaves to help Derek with the kanima.
For the next few days, she keeps her distance from Scott and won't talk to him about his being a Werewolf. He tries to be patient with her but insists that they're going to have to talk sometime. The issue is forced when Gerard Argent and the kanima break into Scott's home and take Melissa hostage. The kanima has her by the throat, holding her up while it clings to the corner of the ceiling.
Scott takes out his claws, but Gerard just tells him to be realistic. Scott asks him to let Melissa go. Gerard says he can't but he might be able to let her live depending on what Scott does. Gerard tells him that he wants Derek and his pack. Scott replies that they're all in hiding, so Scott doesn't know where they are. Gerard thinks that with the proper motivation he can devise a plan, and luckily the kanima is pretty good at motivating people. He can control the kanima because he came to Beacon Hills to avenge Kate, not just bury her.
The kanima drops Melissa, and it and Gerard leave. Melissa begs Scott to give Gerard whatever he wants. Scott explains that it's not that easy.
The next evening is a lacrosse game. Melissa comes into the boys locker room just in time for Coach Finstock's motivational speech. She's confused and taps Stiles on the shoulder. He explains that it's the speech from Independence Day, which is Coach's favorite movie. "He doesn't know any sports speeches?" "I don't think he cares."
Melissa sits with the Sheriff to watch the game, even though neither of their kids are supposed to play this game. Surprisingly, Stiles gets told to go in, and his father wonders outloud why his son is on the field. "Because he's on the team?" Melissa replies. And the Sheriff realizes that Stiles is actually going to play. He's so excited he gets up and cheers just at that.
The Sheriff, Melissa, and Lydia all look mortified as Stiles fails at even the most basic aspects of playing lacrosse.
When Isaac gets injured on the field, Melissa runs out to ask Scott if something more than just a game is happening. He tells her yes, and she tells him to forget what she said before and do whatever he can to help.
Suddenly, Stiles starts to play like he remembers how, and his dad, Melissa, and Lydia all cheer. The Cyclones win the game, but the lights on the field suddenly go out. When they go back on, Jackson is on the ground. Melissa rushes over to help and tells Lydia to hold his head while she tries to get him to breathe.
They declare Jackson dead, and the EMTs load him into a body bag. Melissa gets herself a ride in the ambulance so she can keep an eye on things. At the morgue, she approaches the body bag and sees clear ooze coming out of it. She decides to see what's going on and psyches herself up to pulling open the zipper.
Once she does, she calls Scott. She tells him that she's freaked out and that he should come down to the morgue to see what she found about Jackson. He is covered in a clear cocoon, and his fingernails are shifted into claws.
At the morgue, Scott and Isaac check out Jackson's cocooned body. The body jerks, and they all jump back. Scott asks his mom to zip up the bag, much to her dismay, because isn't her son a big bad Werewolf? She does it, but the zipper gets stuck just under Jackson's chin. Jackson jerks again, and his mouth opens, revealing rows of blackish sharp teeth. Scott implores his mom to finish zipping the bag. She does, and the boys take the body bag and leave.