Rafael made his first appearance in Alpha Pact, when he arrived to Beacon Hills to investigate a slew of grisly murders and kidnappings which, unbeknownst to him, were actually human sacrifices being committed by a Darach named Jennifer Blake in order to get her revenge against the Alpha Pack. He came to Beacon Hills Memorial Hospital to question his son's best friend Stiles Stilinski following an intense battle between the Alphas and the Beacon Hills Werewolves, as they were all fighting over who would get Jennifer Blake in their custody. <
Stiles immediately reacted to Rafael's presence with contempt, suggesting that he had held a grudge against Rafael as a result of his treatment of Scott in their youth. After Stiles lied and said that he spent the entire night locked in the elevator due to the power outage and thus missed "whatever" caused the hospital's destruction, Rafael turned the subject to Sheriff Stilinski and asked why his father had not come into work or returned any of their communications, suggesting that perhaps Stilinski's drinking problem had relapsed again, an accusation that only made Stiles more hostile to him.
The next day, Rafael approached Stiles at school to inform him that his father was officially missing after they had found his car abandoned in the high school parking lot, though Stiles already knew that Stilinski had been taken by the Darach. He tried his best to get Stiles to talk to him, as he knew the boy knew more than he was letting on, but when Stiles insisted that he knew nothing, Rafael released him into Alan Deaton's custody. That night, Scott, Stiles, and Allison Argent were about to perform the surrogate sacrifice ritual that involved the three of them drowning themselves in ice baths and essentially dying in their parents' places in order to find the location of the Nemeton where Chris, Melissa and Noah were being held. However, Stiles, concerned he might not make it back, decided to tell Scott that his father was in town. The scene then cut to the McCall House, where Rafael was sitting in Scott's bedroom, waiting for him to come home and worried about the also-missing Melissa.
In Lunar Ellipse, Rafael and two of his fellow agents went to the Argent Apartment to investigate Chris Argent's disappearance, only to find that it was chock full of weaponry that he and Allison had brought out of storage to use in their battle against the Darach. He then confronted Scott, Allison, and Isaac Lahey when they came to the apartment to get something with Argent's scent to better find him, forcing the three to stay and answer his questions.
However, instead of giving him answers, Allison snidely informed Rafael that her father is a federally licensed firearms dealer and security consultant, which gave him the right to own all of the weapons spread before them on the desk, before she then quickly dropped a smoke grenade to distract the federal agents long enough for the three teenagers to escape. Once Stilinski, Melissa, and Argent were rescued by the Beacon Hills packs, Rafael decided to stay in town a while longer, though it would not be revealed until later that he was actually assigned to stay by his superiors.
In Anchors, it was first hinted that Rafael had official business in Beacon Hills when Sheriff Stilinski and Stiles were talking in Stilinski's office, as Stiles saw a box of cold case files on the floor that read "Deliver to FBI Field Office, Special Agent McCall." When Stiles asked him about them, Stilinski insisted that they needed to talk about something. Later that day, when Scott and Stiles were helping Stilinski investigate a cold case involving Malia Tate, Scott asked Stiles why his father was so intent to solve the case, leading Stiles to be forced to admit that his dad wanted to solve one more case before he was impeached due to Rafael's case.
That night, Scott returned to the McCall House and confronted his father about his case against Sheriff Stilinski, absolutely furious that he would be going out of his way to take away his best friend's father's career. Rafael attempted to explain that his job, which was assigned to him by his superiors, was to put together evidence in order to make a case for impeachment, before snidely adding that it was actually Stilinski's "lack of resolution" and "inability to close cases" that would be getting him impeached, not Rafael himself. Melissa returned home just then and demanded to know what they were fighting about, and she, too, became angry when she heard what Rafael was intending to do. Scott became so upset that he started to involuntarily transform due to the symptoms he was experiencing following the surrogate sacrifice ritual. When Melissa saw that Scott's eyes were starting to glow red and his claws were extending, she insisted that he come with her into the hallway right then, leaving a confused and suspicious Rafael behind to wonder what was going on with their son.
In More Bad Than Good, Rafael showed up with Henry Tate in the Beacon Hills Preserve shortly after Scott and Stiles had found a coyote den with some of Malia Tate's clothing in it and called Sheriff Stilinski in to check it out. Scott, knowing that Rafael was just going to make things worse, tried to talk him down, but Rafael simply stated that he would deal with him later before rudely remarking about Melissa allowing him to run around the woods late at night. After Henry recognized the baby blanket Stiles was holding as having belong to his daughter, Rafael went into the coyote den to investigate it further.
When Stilinski confronted him and admonished him for bringing Henry to the crime scene before they knew what they were fully dealing with, Rafael retorted that Stilinski's reluctance to investigate was starting to make him realize why he had such a hard time closing cases. Stilinski argued that Rafael didn't have the full story, but Rafael replied that with some digging, they should be able to turn up something, such as the bones of a nine-year-old girl. He then went on to add that, for people like Henry Tate, it's the not knowing that hurts the worst, and that the truth, no matter how deeply traumatizing it is, is better than not knowing.
Rafael wasn't seen again until the end of the episode, where, since the Malia Tate case had been closed with Malia's return to her human form from her coyote form, he was walking out of Stilinski's office with his colleagues.
In Galvanize, Rafael was in charge of coordinating the transportation of "the Shrapnel Bomber" William Barrow to Beacon Hills Memorial Hospital for a planned surgery. Rafael instructed one of his colleagues, who was driving the ambulance, to bring him in through the back and to keep Barrow's identity secret, with the exception of those who needed to know.
Inside, Melissa McCall was decorating the nurse's station for Halloween when she saw Rafael striding in and watched Noah Stilinski rush towards him quickly, sighing in exasperation. Stilinski, already knowing why Rafael was there, stated that Barrow would not be coming in, but Rafael argued that this was literally the only hospital that would take him on as a patient; when Stilinski asked about the county hospital, Rafael retorted, "You'd be surprised how fast things fill up when a guy like this needs surgery..." Melissa rolled her eyes at the fact that a patient of this magnitude was turfed to them yet again, and though Stilinski tried to argue that if the county hospital refused to do the surgery, then they shouldn't have to, either, but Rafael insisted that it was because nowhere else would do it that BHMH needed to do it.
Melissa, looking a little green, piped up that someone was going to have to go and do his pre-operation interview, and when Rafael asked her who was normally assigned that task, Melissa sighed and replied, "Me." A short time later, Rafael was walking towards Barrow's hospital room while he was giving a clearly nervous Melissa some last minute advice on how to handle the mass murderer. Rafael reminded her to never forget what he was capable of and recapped the event that landed Barrow in Eichen House's prison-- he was a former electrical engineer who walked onto a school bus wearing a homemade shrapnel bomb, which went off and killed four of the students and left a fifth without legs due to the trauma. When Melissa wondered if his psychiatrist ever made any progress with him, Rafael grimly replied that every day, he insisted that when he got out, he was going to do it again, and this time, do it right.
Rafael, Stilinski, and a dozen other deputies were in charge of guarding the operating room while Barrow's surgery to remove shrapnel left in his abdomen from his previous bombing. They were all shocked to hear Barrow overcome the pain from his surgery and awaken from the anesthesia as he released a swarm of flies from a tumor on his intestines, causing hysteria during the procedure and making it easy for Barrow to grab a nearby scalpel and stab Dr. Vandenberg in the throat with it. Upon hearing the commotion, both Rafael and Stilinski rushed into the OR with their guns at the ready, but they were too late-- Barrow was already gone.
Rafael then organized a small task force to gain information on potential whereabouts for the convicted killer, eventually receiving a tip that Barrow was seen at the train. Just as he was calling out to Stilinski to rally his people and come with him to the train station, Stilinski was pulled aside by Stiles, who informed him that his packmate and long-time crush Lydia Martin had a "supernatural sense" of where Barrow was; Stilinski, appalled, pointed out that Lydia wasn't on the chessboard used to introduce him to the supernatural, but Stiles simply retorted that she was now that they knew she was a Banshee. Despite this revelation, Stilinski decided to follow Rafael's lead, preferring to follow what can be seen with the human eye over a psychic premonition.
Later that night, Rafael was brought up in a phone conversation between Scott and Melissa, as his dinner discussion regarding the Yukimura Family while eating with Kira Yukimura and her parents had led him to think about his own family. When Scott went on to ask his mother why she didn't change her last name back to Delgado after she and his father got divorced, Melissa kindly replied that it was because "McCall" was Scott's name, too.
In Illuminated, Rafael was at the Beacon County Sheriff's Station shortly after the incident at the Electric Substation that resulted in Kira Yukimura inadvertently causing a blackout that affected the whole town, where he and Stilinski were interviewing Kira, Scott, Stiles, and Lydia to figure out what happened.
Rafael began by asking Scott and Stiles what time they got to the substation, and Stiles replied that they arrived at the same time as Scott, but when the follow-up question was, "By coincidence?", the two teen boys decided to play dumb in hopes of confusing and irritating the FBI agent to the point where he wouldn't want to dig any further. After Scott and Stiles debated over who Rafael was specifically asking the question (and Lydia, seeing what her friends were doing, piped up that she assumed he was asking both of them), Rafael sighed in exasperation and insisted that he was the one to answer the questions. All four of the teens gave him a confused and amused look, since they had clearly irritated him to the point of misspeaking, and Rafael gritted his teeth before correcting himself-- "Let me ask the questions."
Realizing that his current tactic wasn't working, Rafael decided to recap what the teens had already told him about what had happened in hopes of confirming that the details were true-- "Just so I have this absolutely clear... Barrow was hiding in the chemistry closet at school. Someone left him a coded message on the blackboard to kill Kira. Then, Barrow took Kira to a power substation and tied her up with the intent of electrocuting her, which blacked out the whole town."
Stiles nodded and stated that this sounded about right, but Rafael simply frowned and asked how they knew to look for her at the substation, leading Stiles to point out that since Barrow was an electrical engineer, it was the location that made the most sense. Rafael, still not buying their story, remarked that this was a "hell of a deduction," with Stiles quipping in response that he gets his skills honestly because his dad is in law enforcement, which makes Stilinski chuckle loudly despite his best efforts to remain professional. After Rafael shot him a dirty look, Stilinski became serious once again and asked his son to simply answer the man's question, and Stiles sighed before reiterating that they had just made a good guess.
Rafael then turned the topic of conversation to Scott and Kira by asking them what they were doing. Since each of them had a different perspective on the dinner they had with Noshiko and Ken Yukimura at Kira's house, Scott said "Eating pizza" at the same time that Kira said "Eating sushi." Realizing that this made it sound like they didn't have their story straight, they immediately switched answers at the same time once again before sighing and echoing each other by pointedly stating "Eating sushi and pizza." Rafael scoffed before looking at Stilinski and asking him if he was really believing the kids' story, and Stilinski joked that he hadn't believed a word out of Stiles' mouth since he learned how to speak before adding that, in this case, he thought Lydia, Scott and Stiles found themselves in the right place at the right time, which was incredibly fortunate for Kira, who survived as a result of it.
Still not convinced, Rafael looked over at Kira and asked her if this was how she remembered it, and she nervously looked at the others before quietly replying "Yes." She then wasted no time asking if she could have her cell phone back, but Rafael denied the request, stating that they had to take it for evidence since Barrow used it. He then informed her that they needed her to fill out some paperwork before they had a deputy take her home safely, dismissing the rest of the teenagers from the room.
As they all left, Rafael caught up with his son Scott in the hallway and stopped him, making it clear that he had no idea why they were lying, or why Stilinski had no issue with covering for them, but that they needed to understand how serious the current situation was. He reminded him that, if the story about Barrow had any truth to it, then not only did someone break him out of police custody, but that the chaos he created was part of their ultimate game. "A mass murderer is bad enough. A mass murderer being controlled by someone? Far worse." Scott, clearly feeling guilty about everything he had to hide from his father, nodded and assured him that he understood, and Rafael eased up a bit, urging him to get home quickly since it was a school night.
Later that day, after Kira revealed to Scott the true reason why she wanted her phone back (because it contained pictures of Kira's strange aura, which Barrow knew about enough to take a picture of her and which could possibly reveal her as being something supernatural), Kira, Scott, and Stiles made a plan to take advantage of the poor staffing at the Sheriff's station due to the blackout and break into the evidence lock-up in order to delete the photos before they could be seen by anyone else. Stiles provided cloned RFID key cards to get into all of the doors but refused to actually participate in the heist due to the fact that he didn't want to get his dad in trouble due to the current impeachment inquiry he was under as a result of Rafael's machinations.
Unfortunately, when Scott and Kira got into the evidence storage, they found that Kira's cell phone had died at some point during the day, forcing them to find a cable to hook up to a nearby laptop in hopes of charging it with the computer's battery (since the blackout was still unresolved by this time). It was then that Scott remembered that Rafael had been using the evidence lock-up as his rudimentary office while working as an FBI liaison and that it was his computer that they were going to use to charge Kira's phone. When the lock screen photograph popped up, Scott was shocked to see that the photo was him and his dad when he was a young child, presumably at the beach together; this seemed to touch Scott, who had always believed himself to be an afterthought to his father.
Meanwhile, Stiles, who was acting as the lookout, became concerned when he saw that Rafael had just pulled into the back parking lot and was about to enter the station before Scott and Kira had a chance to sneak out yet. Cursing under his breath at his luck, Stiles rushed inside and distracted Rafael by rambling a long, drawn-out theory that whoever was controlling Barrow worked at the high school, and Rafael, somewhat impressed, praised him for his smart thinking and pointed out that Stiles' dad was the one who originally gave them the idea.
Just as Rafael was about to walk away, Rafael remarked, "His one useful suggestion," causing something deep inside Stiles to shift and become darker and harder. He then got serious and pointed out that Rafael could claim that his attitude toward Stilinski was all due to professional disapproval, but that he knew the real reason why Rafael didn't like Stilinski. Rafael, skeptical, asked him if this was true, and Stiles confirmed that it was before adding, "Yeah... Because he knows something that you don't want him to know." He leaned in closer to Rafael and whispered, "And guess what? I know it, too," which caused Rafael's face to fall and his expression to become mildly afraid. By this point, Scott and Kira had managed to sneak by them without catching any attention from anyone, allowing Stiles to finally leave the building and return to his Jeep. However, Rafael was not shaken up enough not to notice that the door to evidence lock-up was still open.
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In Letharia Vulpina,
In The Divine Move,