THE PROTOCOL SERIES

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The story is set in a near-future world shaped by the Standstill, a prolonged slowdown in technological advancement accompanied by an increasing dependence on automated systems that humanity has grown too comfortable in. It opens in Babylon, New York, with the death of Hannah Morgan, a woman who has lived with chronic medical complications caused by prenatal drug exposure. She receives medication from an automated pharmacy system that has been subtly but precisely altered. While driving, she loses consciousness and presumably dies in a collision. The pharmacist who dispensed the medication, Ron Lupin, realizes that something is wrong and repeatedly attempts to contact her. When he is unable to reach her, he turns himself in and is detained while the police investigate.

Hannah’s autopsy is performed by Abigail Warren, a medical examiner, who concludes that the dosage error shows signs of intentional modification. She determines that Hannah experienced a heart attack and died before the collision, citing the modifications of the medication as the cause. Abigail also observes her phone briefly malfunction at the crash site, unaware that it has been silently compromised. Hannah’s daughter, Rebecca Morgan, who lives in Mayberry, Tennessee, later receives her mother’s phone. Sean Caldwell, a highly-skilled computer programmer who lives in Applewood, Tennessee, and attends Hybrid-Tech University alongside Rebecca, offers to examine Hannah's phone after hearing the story from his friend, Dustin Hill. Rebecca urgently accepts Sean's help in hopes of uncovering the truth. Later that night, Abigail is awoken by her electronics behaving erratically, the virus from her phone having infected them. She contacts her brother Jake, who initially responds dismissively before arriving the following morning, presenting himself as unserious and childish, complaining about driving through a thunderstorm.

When Sean runs a script to detect erased data, the program completes instantly, skipping several steps. Running it a second time reveals intentional system alteration and the removal of call records. Sean determines that Ron attempted to contact Hannah multiple times, and left voicemails that were deliberately erased. Unbeknownst to Sean, his computer and storage devices have already been infected. After research and investigation into the mysterious virus, Sean begins to suspect a connection to Protocol: an adaptive, artificial intelligence experiment that was shut down and abandoned months ago due to nearly causing a nuclear launch. He believes it has somehow reactivated or been rewritten, and has learned how to bypass automated safeguards. Protocol altered the automated pharmacy subtly enough to cause Hannah's death, infected her phone, and erased the evidence of Ron's attempts to reach her, causing Hannah to become the first confirmed fatality of a rapidly spreading techno-biological contagion.

Following his arrest, Ron is detained by Jim Dalton, who appears sympathetic, while expressing contempt for the systems involved, loudly criticizing the entire police department for withholding the freedoms of an innocent man. Ron is incarcerated for a week due to unresolved evidence and the anger of Darren Morgan, Hannah’s husband and Rebecca's father. Jim releases Ron to speak with Darren, who claims that Hannah's phone had no contact records of any kind. Rebecca then contacts her father and explains what Sean has uncovered, saving Ron's freedom just in time. Darren absolves Ron and prepares to travel south to Mayberry to see his daughter. He invites Ron to accompany him, emphasizing that the decision is voluntary. After deliberation, Ron joins Darren, unable to stay away from the mystery.

During their drive, Protocol spreads from Ron’s infected phone into Darren’s patrol car and surrounding infrastructure, creating a widening pattern of failure. Darren and Ron encounter increasingly disturbing anomalies, including autonomous vehicles behaving erratically. At one such incident involving a utility van crashing into a closed restaurant, Darren narrowly avoids knocking over a young girl. A woman identifies the child as her niece and dismisses the incident before leaving. The girl, Monica, responds playfully to being scolded. Ron and Darren bond during the road trip.

A few days later, the same woman, Amanda, is shown caring for her sick niece, Monica, in Applewood, Tennessee, who is undergoing treatment for Merkel-cell carcinoma. Her father has been absent from her life for several years. Amanda brings Monica home with her from a hospital for sick children, and they have a night of fun together. Later that night, Monica is awakened by a bright light and a low humming outside her window. She quietly sings “Twinkle, Twinkle, Little Star,” her favorite nursery rhyme, before returning to bed. The light intensifies, and she awakens again to find a small, frail being looming over her. Paralyzed except for her eyes, Monica is unable to scream as the being inserts a metallic bug into her ear. She awakens the next morning feeling nauseated and altered, unable to explain what has changed. Amanda soothes her as a thunderstorm passes outside.

Meanwhile, Sean receives troubling medical news regarding a possible abnormality detected in his brain. Although his doctor, Daniel Connors, cautions that the finding may be benign, he warns of possible hereditary implications. Using the doctor’s computer, Sean runs a script designed to search for known elements of Protocol’s architecture. Protocol is briefly quarantined, but it adapts and escapes containment. Sean is immediately detained by federal agents led by Special Agent Winona Reyes. Once Sean is taken away, his distant father, John Caldwell, emerges and arranges for Sean to be inducted into GAIA, the Global Alien Intelligence Agency.

Sean is brought before President Derek Matthews and is instructed to run his script on government supercomputers, which identify Protocol’s origin at the NSA within seconds. Sean accompanies Winona and President Matthews to the facility, where agent Dale Winston reveals that the NSA was infected while surveilling a SETI researcher with a criminal history, William Donovan. The virus, a modified version of Protocol, spread from the NSA to public digital systems around the globe that the NSA were tapped into. William arrives after detecting the intrusion himself, telling of an extraterrestrial frequency identical to the Wow Signal that was received shortly before Hannah’s death, suggesting Protocol may not have originated on Earth. The president provides Sean with an unredacted GAIA dossier, asking for his help. Sean is then sedated and later awakens at home with the folder in his possession. John emerges from behind President Matthews and boasts about choosing Sean for GAIA.

Darren and Ron are secretly implanted during their journey with metallic bugs, programmed for delayed activation, during an alien abduction they don't remember, and experience missing time. Ron received one in his wrist, and Darren received one in his neck. Upon arriving at Rebecca’s home in Mayberry, Ron begins compulsively scratching at his wrist. Despite Darren’s warnings, Ron exposes the metallic bug, which activates and multiplies into a swarm that consumes him from within. Darren exits the vehicle and watches as the swarm recombines and collapses into the passenger seat. Darren secures the metal bug while suffering electrical shocks, then checks his itching neck, but dismisses it. Rebecca comforts her father afterward, and Darren asks her to contact Sean.

Sean receives Rebecca’s message while struggling with grief over his late wife, Clarissa. He experiences a hallucination of Clarissa, urging him to go to Mayberry to help Rebecca and Darren. Afterward, he calls Dustin, who encourages him to make the trip. During the drive, he pulls over into a restaurant's parking lot and dials his sister, Amanda. He tells his sister the story of how Clarissa was murdered by a burglar who got into the house, when Sean left after a heated argument, and how guilty he feels about it, stating he gave Monica to Amanda because he couldn't handle seeing Clarissa in her eyes, and he didn't want to fail her too. He acknowledges his absence as a father, and resolves not to be like his own father, John. After speaking with Monica, Sean learns that Amanda has been covering for him by telling Monica that Sean is a spy like James Bond. Amanda tells Sean that their dad called, and though he initially feels resentful, he concludes that he must forgive his own father if he wants Monica to forgive him.

Sean travels from Applewood to Mayberry, and during the drive, he gets the idea of diplomacy and communication. When he arrives at Rebecca's house, he reconnects with Rebecca and meets Darren. Together, they agree that attempting communication first rather than escalation may be the only viable response to the unfolding crisis. Sean and Darren quickly bond, with Darren gradually becoming a father figure to Sean.

When Darren asks Sean about a way to send a diplomatic message to aliens, Sean recalls his estranged friend, Kyle Wills, known as "Wheels," a car enthusiast and avid UFO conspiracy theorist, who merges automotive and digital systems. The group travels to Kyle’s home, where Kyle reveals ANNI, an Artificial Neural Network Intelligence embedded in his car, designed with strict ethical constraints. Sean and Darren draft a message intended to reach the same satellite from which the modified Protocol originated.

Meanwhile, Abigail delivers a public address, explaining that nanotechnology is spreading silently through technology and medication, mimicking illness and causing widespread misdiagnosis. She notes that certain sound frequencies seem to disrupt the nanotechnology as Sean, Darren, Rebecca and Kyle listen to the speech during a test drive in ANNI. While listening to Abigail’s speech, a swarm of metallic bugs rises from the road and assembles into a metallic humanoid form. Initially under unknown control, the entity is overtaken when ANNI broadcasts the diplomatic signal. A separate external intelligence takes control and responds, agreeing to send a representative to the White House for a formal parley, stating that they created the metallic bugs, which they call biobugs.

Following Abigail's speech, Astro, a covert faction within GAIA, discusses silencing Abigail. Jake overhears the conversation and attempts to warn Abigail, but her phone dies and her house loses power. Carl Windell, an agent of Astro, arrives at Abigail’s home. Jake intervenes, revealing his affiliation with GAIA, much to Abigail's surprise. Carl provides limited information about a mysterious figure known as the Channeler, and Jake uses a teleportation device to send Carl to a GAIA holding cell. Jake later informs Abigail that he has been ordered to initiate Sean into GAIA.

The group returns to Kyle’s home, where Darren grows increasingly distressed about the implant in his neck. Attempting to remove it himself, Darren triggers its activation under a different directive. He later confronts the group in a controlled state, before being incapacitated when Sean and Rebecca use ANNI to broadcast a disruptive frequency that ANNI located from Abigail's speech, while Kyle acts as a distraction. Once Darren is subdued, Sean, Rebecca, and Kyle reassure him that he was acting under external control, and that he bears no responsibility for his actions.

Jake and Abigail arrive with additional intelligence and introduce themselves to Sean, Rebecca, Kyle and Darren. Kyle bonds quickly with Jake, and Rebecca bonds with Abigail. Kyle and Rebecca read the GAIA dossier aloud, revealing GAIA’s origins, the Kriff (known to humanity as the Grays), and a conditional surrender allowing human abductions in exchange for survival and technology. The dossier contains details about Project Longshot, initiated in 1990, a probe that reached an alien homeworld in 2034. Despite John Caldwell’s warnings about a cloaked planet, the probe detonated a massive fuel reserve after being pulled into the planet’s gravity well. The aliens re-transmitted the Wow Signal as a cry for help and fled toward Earth, which the signal did not reach until 2036.

Before traveling to the parley, Sean asks Rebecca to call Amanda, and requests that she and Monica travel to Kyle’s home for safety. During the drive, Amanda is blinded by a brilliant light in the sky, and another vehicle collides with her SUV. Amanda survives, but Monica disappears. At the parley, John’s presence causes a strained reunion with Sean. An alien emissary, Eco'Corulaz, phases through the ceiling, and calls his people the Nephilium, saying that the humans may call him Echo. He confirms that Nephilu (pronounced neh-FEE-loo), the Nephilium homeworld, was destroyed by the Longshot probe. He informs the group that, upon reaching Earth, the Nephilium accidentally reactivated Protocol by rewriting it to disable digital infrastructure, as they didn't want humanity to attack them, unaware of Protocol's adaptive nature. Protocol spread globally, and the Kriff later seized control of the biobugs. Echo and his people are able to contain Protocol to prevent further spread, but he states that damage already done cannot be undone. He then agrees to accompany the group back to Kyle’s home, and John travels with them in a separate car.

After talking to Amanda on Sean's phone in a separate room, Darren tells Sean about Monica's disappearance. Sean reacts immediately and talks with Echo, who has a way to rescue Monica from the Kriff. Sean lets John perform the debrief of the parley instead of himself, asserting that Monica is more important. President Matthews announces the death toll to the public, which is over four billion lives. Monica is rescued by Sean and Echo using a sound-based resonance device on the Kriff vessel. Sean notices that Monica's hair has grown back, and Amanda suspects that Monica's cancer has somehow been cured. Jake later overhears John admitting that he leaked Monica’s location to test the resonance technology. Jake attempts to warn Sean, but their confrontation escalates into a violent fight, leaving Jake critically injured. Echo heals Jake, but explains the limits of his abilities. The Kriff adapt to the resonance frequency, rendering it ineffective, inflicting heavy losses, and leading to a new strategy after a regroup.

After the initial loss, Amanda, Whitney (Sean and Amanda's mother and John's wife), and Monica are brought to the GAIA base. Sean devises a plan to invert Protocol's experiment by turning it inward toward the Kriff. They plan to use Nephilium nanotechnology to teach the AI, instead of it learning on its own, and ethically contain it. During the final battle, John leaves safety to fight directly in an attempt at redemption and is gravely injured. Echo stabilizes him temporarily, but he is unable to fully heal him. Another Nephilium, Dephilius, transports John to another world where healing may be possible. John instructs Sean to tell others that he's in the stars.

As the conflict escalates, the Nephilium regain control of their biobugs and deploy them against the Kriff, shutting them all down. Zanu, one of the last original Kriff leaders, is defeated by Sean and Echo by using a chess concept called zugzwang. In the aftermath, Abigail uses Monica’s altered blood to synthesize a global cure for cancer, GAIA continues operating, Sean declines becoming GAIA's director for a year to focus on his family, Winona Reyes becomes Acting Director, and Jake is reluctantly reassigned alongside his girlfriend, Melinda Mayfield. Abigail also becomes GAIA's first field medic, now actively saving people with her own team instead of after it's too late. After outperforming Jake's scores in physical and mental testing, Melinda begins searching for the Channeler alongside Jake.

The story concludes with Monica singing "Twinkle, Twinkle, Little Star," while gazing out a window at what appears to be a star, revealed to be a surviving Kriff vessel. Inside, President Matthews is restrained as Jim Dalton emerges from the shadows, revealing himself as the Channeler, while biological Kriff watch over the president. They depart for Saturn, telling Derek Matthews that they have big plans for him. Monica finishes the song and opens her eyes, now black like a Kriff’s, suggesting that she may be a human/Kriff hybrid.

The epilogue takes place on Christmas Eve, 2041. Sean and Rebecca bake pastries while Monica plays in the snow. Their four-year-old son, Jonathan, refuses to join her and runs upstairs. A knock sounds at the door, and Sean opens it to find an older version of Jonathan standing outside. 

Sean Caldwell – The main protagonist and computer programmer who discovers the truth behind Protocol, becoming central to humanity’s survival, and eventually, Rebecca's love interest. He is a widower after the murder of his wife, Clarissa, and the son of John and Whitney Caldwell. His ethical inversion of Protocol and preference of communication over domination serves as the answer to the novel's core problems. The president makes Sean Acting Director with John MIA at the end of the story, though Sean temporarily declines this for a year to focus on his family first, allowing Winona to fill the role. Sean is caught between individual ethics and institutional duty, and must choose who he wants to be. His initial abandonment of his daughter presents him as an imperfect and flawed hero, rather than a purely "good" or "chosen one" character.

Amanda Caldwell - An elementary school teacher, Sean's sister, and the caretaker and protector of Monica. Amanda holds a strong contempt for her brother after his abandonment of his daughter, though she doesn't know the full story until later. She covers for her brother by telling Monica that Sean is a spy like James Bond, and that Sean can't be around Monica because it's too dangerous. Amanda is based on Zollern's real-life half-sister, who died while pregnant when hit by a drunk driver.

Monica Caldwell – A nine-year-old girl suffering from Merkel-cell carcinoma and Sean’s daughter, whose mysterious transformation plays a key role in the story’s conclusion. Monica serves as humanity's innocence that must be saved, and the line that must not be crossed. Her first name is the first half of a reference to a character from The X-Files, Monica Reyes. Her favorite nursery rhyme is "Twinkle, Twinkle, Little Star," a recurring motif and poem throughout the story. Zollern wrote a darker version of the poem, and two lines of it are presented before every chapter, intended to transform innocence and curiosity into cosmic dread. Her character was inspired Zollern's real-life niece, who was stillborn after the wreck that killed his sister.

Rebecca Morgan – An astronomy student and Sean's love interest, who is investigating the circumstances surrounding the death of her mother, Hannah Morgan. Sean approaches Rebecca in a hallway in college during her breakdown while holding her mother's phone. She is an emotional anchor who uses grief to motivate her search for answers, helping to move Sean forward past his grief and loneliness. When Sean offers his help, she accepts it urgently.

Darren Morgan – Rebecca’s father and a sheriff of the Babylon Police Department struggling with grief and responsibility. Darren contrasts John's emotional absence and institutional authority by being emotionally present and focusing on individuals first. He is grieving the loss of his wife, Hannah, and later, his friend, Ron. He gradually becomes a father-figure to Sean, serving in the capacity that John could not. Though slightly paranoid, his philosophy is that if we don't maintain our humanity, then we aren't worth saving. His character was originally inspired by Robert Patrick's character, John Dogget, from The X-Files.

John Caldwell – Sean and Amanda's father, Whitney's husband, and the secret director of GAIA, the Global Alien Intelligence Agency. John was emotionally absent from Sean's life, choosing work over family, believing that keeping the world safe made up for his failures as a father. John has good intentions, but handles situations in ethically compromising ways. He oversaw Project Longshot, the probe that destroyed Nephilu due to Kriff manipulation. Despite his warnings to his agents to abort, they pressed on, and John chose to keep it buried, believing the secret would die with the Nephilium homeworld. John's fate is left ambiguous after he is fatally wounded and transported to the stars by the Nephilium, Dephilius. Zollern's real father died a year before the story's completion through a sudden health crisis, and though it was originally planned for John's character to die, Zollern changed his mind as a way to keep his father alive. John later instructs Sean to tell others that he is "in the stars." This connects to the dedication at the end of the book, where Zollern acknowledges his father by saying, "We love and miss you, Dad. I hope you're reading this in the stars." Zollern's father was also emotionally distant and frequently put work first, leading to a strain on their family, and is described as feeling like the weight of the world was on his shoulders. This is what John's character was modeled around.

Whitney Caldwell - John's wife and the mother of Sean and Amanda. Whitney brings hope and motivation to the group near the end, though she is a heavy force to be reckoned with, even intimidating John. Her character is inspired by Winona Rider from Aliens and Stranger Things. Her grief over losing John is explored in the next book in the series. The words she yells at John as he's dying are the same words Zollern's mother said to his real father as he passed.

Hannah Morgan - Darren's wife who tragically dies from faulty medication generated by an automated pharmacy. She suffered from prenatal drug exposure, leading to multiple health issues in her adult life, including a heart attack. This heart attack is what leads her to grabbing faulty medication from the automated pharmacy, serving as the catalyst for the story.

Kyle "Wheels" Wills – Sean’s estranged friend and the creator of ANNI, an artificial intelligence embedded in his car. Kyle is an avid UFO conspiracy theorist who lost many friendships and relationships due to his unconventional beliefs. When he is proven right, he's overwhelmed by the connections he's lost because of his need to be right, not finding the vindication he had hoped for. Kyle prefers to be called "Wheels," due to its similarity to his surname and his affinity for cars. Sean and Kyle lost contact for years due to Sean's abandonment of Monica before they reconnect in the story. Kyle has a penchant for giving nicknames to people and places based on their words or actions, especially first impressions. Examples include calling Sean "Gandhi," and "Will Robinson," referring to Darren as "Cat Daddy," "the geriatric T-1000," and "psychotic Andy Griffith," calling Jake "State Farm," and referring to the GAIA base as "Hotel California." Parts of his personality are loosely based on Zollern's real-life best friend.

ANNI - An Artificial Neural Network Intelligence embedded inside Kyle's car, using fragments of Protocol's code, but ethically constrained. She functions as the Elie Arroway of the story, and is a reference to Contact (1997), Eureka (2006 - 2012), and Knight Rider (1982 - 1986). Playing the signal on the remote highway is what leads to Echo's later arrival, because the group focused on diplomacy first, suggested by Sean. Her appearance is described as a black, 1969 Chevrolet Chevelle Super-Sport with a red, leather interior, red trimmings, red rings around her rims, two bright, white stripes down the middle of the car, and a front license plate that reads, "ANNI."

Abigail Warren – The medical examiner who first identifies anomalies in Hannah Morgan’s autopsy. Abigail is a classy but isolated lover of literature who later disseminates the truth about Protocol's nanotechnology, though she has no knowledge of extraterrestrial involvement. She begins the story determining how people died, and later becomes someone who helps prevent people from getting that far. She was initially based on Gillian Anderson's character, Dana Scully, from The X-Files, who Ron explicitly references as a joke after his abduction by the Kriff with Darren.

Jake Warren – Abigail’s brother, who is known for his humor and wittiness. Jake later reveals to his sister that he is a secret agent of GAIA, and has been working to keep her and everyone around her safe. Jake uses humor as emotional armor and as a mask for competence, using levity as restraint in dark times. He frequently says whatever's on his mind, and can be a bit eccentric with minimal patience. This directly contrasts Winona's personality of control. His role in the story is presented as drama relief, while still maintaining the stakes of the story. His mask of humor and levity breaks twice: once when everyone around him loses their way, and again when his girlfriend, Melinda, pretends not to know who he is, emphasizing the seriousness of the situations when the "funny guy" stops being funny. He is loosely inspired by a Halo character named Buck, voiced by Nathan Fillion.

Winona Reyes - A high-ranking GAIA agent undercover in the FBI and Jake's work partner, who initially detains Sean. Her personality of control directly contrasts Jake's personality of chaos. She later fights with humanity against the Kriff during the final conflict. Her surname is the second half of a reference to a character from The X-Files, Monica Reyes. Winona is professional, but always serious, and acts on impulse, with little patience for Jake's childishness. She frequently masks her humor and emotions behind seriousness, believing the mission must always come first. She is made Acting Director by Sean after he declines directorship for a year to focus on his new family first.

Melinda Mayfield - John's right-hand woman, and Jake's girlfriend, who controls finances, human relations, and anything related to GAIA that John needs. She is later reassigned to be Jake's new work partner when Sean makes Winona Acting Director, much to Jake's concern. She is critically injured before being healed by Scarlet, and plays a joke on Jake by pretending she doesn't know who he is. This is one of two times in the novel when Jake's humor disappears, emphasizing the seriousness of the situation. She changes her last name to Lopez in the second book.

Eco'Corulaz / Echo – A blue-skinned Nephilium emissary, whose empathy for humanity distinguishes him from his species. He tells members of the parley that humans may call him Echo. Throughout the story, Sean repeats a quote, saying, "we call him Echo." Echo serves as a way for humanity to see itself from an outside perspective, and an "echo" of what humanity could be if properly guided. He later calls Sean his "best friend," an Earth sentiment he adopts, and later asks Sean to be the human ambassador for the Nephilium race. Parts of his character are inspired by Spock and Data from Star Trek, especially his friendship with Sean, who says that they will be friends "now and always."

Kli’Cacowas / Klick - A green-skinned Nephilium who assists humanity with the crisis alongside his mate, Scarlet.

Sca'Lorit / Scarlet - A red-skinned Nephilium who assists humanity with the crisis alongside her mate, Klick.

Dephilius - A purple-skinned Nephilium who arrives to take John to the stars in hopes of healing him after his fatal injury, leaving John's fate ambiguous.

Jim Dalton / The Channeler - A police officer and Darren's deputy at the Babylon Police Department, who initially presents himself as friendly and sympathetic, but is at the end of the story to have influenced events by working with the Kriff as the mysterious figure known as the Channeler. His character is explored deeply in the second book of the series.

President Derek Matthews - The President of the United States, who knows of GAIA's existence, but cannot access their classified files or grant access to others. He recruits Sean to use government supercomputers to track the origins of Protocol, which they discover at the NSA. At the end of the story, the Channeler has him restrained to a metal table with the Kriff, and departs for Saturn.

William Donovan - A SETI researcher, who investigates an anomaly in a satellite orbiting Earth, and receives a signal from space matching the Wow Signal from 1977. An agent of the NSA, Dale Winston, was tapped into William's computer as he diagnosed the problem, and Protocol spread to his computer during the investigation after the satellite rebooted itself.

Dale Winston - An NSA agent tapped into William's computer as he investigated a digital anomaly in a satellite orbiting Earth. Once William's computer became infected, it spread to Dale's, whose team tried to study the virus while it was in quarantine. However, the virus escaped through the NSA and digitally infected the global population, a fact the government kept secret. This was presented as "a consequence of violating people's privacy."

Ron Lupin - The pharmacist who dispenses Hannah's medication from an automated pharmacy. He initially doesn't realize the medication is faulty, leading to Hannah's death. He tries contacting Hannah multiple times before discovering later that she died in a wreck, and that all of his attempts at communication were erased. Ron and Darren bond and become friends before Ron's sudden death by a swarm of biobugs, which Darren and Rebecca witness. The purpose of his character is to show that individuals pay the price when technology and its creators aren't held accountable.

Carl Windell - A British member of Astro, a secret organization operating within GAIA as an insurrection working for the Kriff. He was abducted as a young boy and forced to work with them, eventually receiving super-strength from Kriff experiments. Carl reveals the existence of the Channeler and the presence of another alien race (the Kriff), who have been on Earth since 1947, a fact that GAIA and the U.S. government have kept secret. When Carl threatens Jake's sister, Abigail, he uses a weapon to teleport Carl to a GAIA holding facility, revealing his affiliation with GAIA to his shocked sister.

Professor Howard Foster - Sean's cybersecurity professor who coins the term, "the Foster Principle," which later inspires Sean to invert Protocol's programming directives toward the Kriff. Though he only appears in one chapter, the Foster Principle is crucial for the story. His last name is a reference to Jody Foster, who played Elie Arroway in Contact (1997). His classroom scene was inspired by Nicolas Cage's role in the movie Knowing (2009).

Doctor Daniel Connors - Sean's doctor, who was also the doctor for his father since John was young. He explains the implications of the alleged mass in Sean's brain, citing that there could be heredetary implications if the cancer was real, a hint to Monica's cancer. The doctor also mentions a patient from thirty years prior who had undeveloped fetal tissue at the base of his brain, and who had deep claustrophobia. This references Zollern himself, as it details his own experience, whose mother had two miscarriages before having him.

Gaia - A member of the Progenitors, an alien race that created humanity and the Nephilium, described as twenty-foot tall, glowing beings, some of whom have wings. She makes herself known to the Alien Interception Unit (AIU) in 2025, stating that she is "checking on her children," and warns of a global catastrophe coming in 2036 (the events of the novel). The AIU adopts Gaia's name and rebrands after this encounter. The Progenitors will be featured throughout the series, particularly in the third book.

Zanu - A biological Kriff leader, who Kyle and Sean interview. Zanu reveals that the crahsed UFO in Roswell, New Mexico, in 1947, contained a failed Kriff clone, which served as humanity's first technological breakthrough in AI, later evolving into Protocol. Zanu states that the Kriff initially were on Earth when the pyramids were built, as they were fascinated with the concept, but soon discovered that humanity contains a genetic code that would allow the Kriff to once again biologically reproduce. They have been relying on cloning for centuries, and only six biological Kriff remain. This includes Zanu, who mentions that nuclear war eons ago is what caused their reproductive stagnancy. Sean and Echo defeat Zanu by using a chess concept called zugzwang, using the fact of the Kriff being clones against it. Kyle's interrogation of Zanu serves as a subtle reference to Area 51: The Alien Interview (1997).

Jonathan Caldwell - Sean and Rebecca's young son in the epilogue, who arrives as an adult from the future at the end of the novel. Jonathan underwent a mysterious experiment called the Beta program, the motives of which are left ambiguous. He is the core character of the next book in the series, The Escapement Paradigm, which deals with time travel. The character is reused from another story Zollern scrapped in 2011, named Jonathan Beta. That version of the character was the son of an alien / human hybrid woman named Bailey, and he was the leader of the Galactic Armored Interception Agency. GAIA was a concept that was re-imagined for The Protocol Experiment. Zollern wanted to use the character after having him "sit on the shelf" for so long, and to leave the story open for a direct sequel.