It is April 6th, a Saturday morning forty years after Martin Luther King voiced his dream of an America where content of character defines an individual's worth. Yet even as many Americans have been raised on that dream, dawn breaks over the City of Angels shining onto proof that King's dream has not been realized. On the gigantic letter "Y" that is part of the famous Hollywood sign hangs a young man whose life ended in violence. Hanging from his bound wrists, the youth is beaten and bruised with the word "mutant" carved into his chest. This is the America of today.
The next morning in Washington DC, Catherine Gray awakens from her nightmare of a burning baby begging her to wake up. After a few moments of silence, Catherine's cell phone rings. Catherine answers the call and hears her partner Aaron Kearse on the other end. Kearse tells Gray that their boss, Green, wants them in Los Angeles as soon as possible on the Hollywood sign case. As she gets ready, Gray asks Kearse if there has been an autopsy yet. Kearse, likewise getting ready, tells her that the preliminary examination reveals six gunshots to the chest, massive blood trauma and considerable blood loss from the carving in the chest. After Gray asks about the police report concerning burns, Kearse confirms that there were burns on 60% of the body. Taking a pause, he asks Gray if this is going to cause a problem. Gray replies that it will not, and tells him that she will be at the airport in an hour. After hanging up with Gray, Kearse turns to his wife and asks for help with the tie he has been struggling with. As she helps him, Kearse tells his wife that soon he will be able to do this again by himself. Finished with the tie, Kearse's wife points to her husband's shriveled arm and laments that she was just beginning to enjoy dressing her handicapped husband. Placing her arms around her husband, she asks him to promise to be careful.
Hours later, in front of a crowd of reporters and spectators, Chief Murray of the LAPD introduces Aaron Kearse and Catherine Gray of the FBI's Mutant Civil Rights Task Force. He informs the crowd that they will be assuming the lead role in the investigation into the murder of William Sumner and pledges the department's full cooperation. Taking charge of the press conference, Kearse tells the crowd that they are actively pursuing a number of leads and continue to encourage anyone who has information to come forward. Next he introduces Helen Sumner, the mother of the slain youth, and vows to doggedly pursue the person or persons responsible for her son's murder.
Finally, Kearse begins to explain that the MCRTF was recently formed in response to the increase of mutants in the country as well as the increase of hate-driven crimes against mutants. As Kearse continues to speak, Gray hears another voice, not Kearse's, inside her head. The voice tells her that she is the redhead in the back. Jean Summers, the telepathic redhead, tells Gray that she wishes to give a simple warning: They are watching them. They don't trust the FBI, the "task force", and certainly not her partner. His thoughts are dark, his soul tortured and his heart knotted with hate. Lastly, Jean tells Agent Gray that there are those who wish to see no harm come to her, hence this warning. Jean gives the final warning of telling Gray to watch herself, before releasing her back to reality. Now once again cognizant of the events around her, Agent Gray is pulled aside and informed of a break in the case regarding a mutant hate cell based in the valley.
In the San Fernando Valley, north of Los Angeles, FBI SORT team awaits its orders under the cover of night. Chief Murray informs Kearse that the subject's name is Alex Clowes. After noticing a suspicious vehicle, a Hollywood Hills resident reported the license plate that has led to Alex Clowes. Now holed up with a suspected twenty others, Clowes has a record of mutant harassment. With the order given, the team breaks down the front door and rushes inside. Among the blaring Slim Shady music, they find pot, beer, hate literature and six crates of automatic weaponry, the agents find Alex Clowes. They ask Clowes what he planned to do with the weaponry or the map detailing the next week's Mutant Pride Parade through Glendale. Sensing the connection. Chief Murray asks Clowes if he had decided to get a jump on the fun by crucifying Billy Sumner on the Hollywood sign. To Kearse's surprise Clowes tells him that Sumner was not only not a mutant, but was part of Clowes‘ group.
Sometime later, in the LA County morgue the pathologist, Mike, discovers something odd within the corpse of Billy Sumner. Finding a liver that did not belong to him, but to a mutant, Mike supposes that Sumner must have been one of the "Third Species nuts" who try to become superhuman by having mutant organs surgically implanted. A short time later, Agents Kearse and Gray inform Mrs. Sumner of the situation. Shedding tears of joy, Mrs. Sumner thanks the agents for the information that her son was not a mutant. As she walks away, she tells them that Billy's father was so ashamed he wouldn't even come, but now ...
Later in his hotel room sitting on his bed, Agent Kearse looks back and forth between a medical book and the Bible, turned to the book of Genesis, while speaking to his wife Amy on the phone. Amy asks why the FBI is keeping them there if the boy wasn't a mutant. Kearse explains that Green wants to avoid seeming to say that "transgenetives" don't deserve justice as well as normal people. Trying to cheer her husband up, Amy tells Kearse that his son made something for him that should cheer him up. He asks what it is, but she rebuffs him, saying that their son wants it to be a surprise.
Agent Kearse awakens in his hotel bed to the sound of the ringing phone. On the other end is Agent Gray. She informs Kearse that they she has received a call from Tippy Kingston, the publicist for Sterling Whitman. The publicist informed her that Whitman has some information that can help them and wants to see them ASAP. While examining his shriveled left arm, Kearse tells Gray that he has one question: Who the heck is Sterling Whitman?
As they arrive at Whitman's mansion in Malibu Hills, north of Los Angeles Gray explains that he made his first millions financing "blaxploitation" movies and then moved into so-called "socially conscious" movies that won several Oscars. After ringing the doorbell, Gray takes a moment to ask Kearse if he noticed the redheaded white chick at the press conference the previous day. Kearse replies that he didn't. The door opens and Tippy Kingston welcomes the two agents and invites them inside. She leads the agents through her employer's mansion which she explains is in the middle of renovation. The plan, she says, is to turn over the area to mutant artists to make his fabled City on the Hill into a mecca for mutant culture. As they pass through a hall adorned with movie posters of Whitman's making, Tippy points out the "Black Rose", an early cultural watershed in terms of bringing an African-American heroine to the screen. Agent Gray, a black woman herself, rolls her eyes at the poster of "Black Rose" and mutters that it is a "real classic". Moving to another movie poster the guide shows the banned in theaters / direct to video movie "Hero X". She explains that it was Whitman's first project into mutant cinema.
The trio emerges on the backside of the mansion near the swimming pool. Gathered around the pool are two dozen or more people, mostly mutants enjoying the pool, drinks and the weather. The guide introduces the two agents to Sterling Whitman. Whitman welcomes the two to his "City on the Hill". Instinctively, Whitman stretches his hand out to Kearse for a handshake, only to realize the agent's physical deformity. He apologizes and the mistake is dismissed. Whitman recalls to Kearse that his injury was from an encounter with a mutant. Kearse tells him he is correct and asks how he knew. Whitman explains that Agent Murray, whom he employs as a consultant, told him. Next Whitman turns to Agent Gray and tells her that he knew her mother very well from the days when the City on the Hill was a sanctuary for the Civil Rights movement. After he asks how her mother is doing, Gray ends the conversation by informing him that they have not spoken in years. Getting to the point Gray asks Whitman what information he has for them.
Whitman points to his nearby son, Malcolm, who in half emerged in the pool. Whitman explains that Malcolm suffers from a rare disease that cause his skin to blister and spend most of his time in the pool to remain comfortable. Continuing, Whitman says that during production of the film Hero X, Malcolm became close to Billy Sumner; very close. However, at the time, they knew Billy as Nathan Plummer. A week ago, the two had a falling out. Now, Whitman says, they might want to question his son, but instead of the mental and legal trouble, he presents them with a dossier prepared by his lawyers. The dossier includes a hand written statement from Malcolm with everything that they know about "Nathan Plummer". Handing the envelope toward the agents Whitman begs them to let it stand as their only cooperation and to leave his son alone.
Noticing that the agents stand unmoving to the offer, Whitman asks if they would reconsider if he made it more worth their while. Gray is shocked at the blatant bribe, but Whitman asks to rephrase. He is creating a television show about FBI agents investigating mutant civil rights abuses, which would need highly paid FBI consultants. Acting incredulous, Kearse asks Whitman if he is aware that it is illegal to bribe a law enforcement officer. Interrupting the swiftly degenerating conversation, Tippy announces that Police Chief Murray has called. Murray had told her that an arrest has been made and asks for the agents Kearse and Gray to return. As they leave Gray tells Whitman that the thing that her mom liked about him was that he wouldn't know a Black Panther from a black jaguar. She asks him if he knew what she meant, and Whitman says that he does not. As the agents leave they decide to call Green to expedite a search warrant.
Later at Police Plaza One, Chief Murray chastises Gray and Kearse. He tells them that during the time they took to return to the station, Whitman has contacted every prominent public official in town to complain about their "Gestapo-like questioning tactics". Turning to Gray specifically, he wonders if her outburst whether she has already compromised the investigation. Cutting the conversation off, Kearse asks Murray about the suspect they have behind the one-way mirror. Murray explains that they received an anonymous tip that gave them the same information Whitman just gave them... and more. The suspect's name is Dean Crawford and he also worked on the Hero X movie. Also, like Malcolm Whitman, he got friendly with Nathan Plummer. For the past hour, Murray informs them, they have been questioning him, but he refuses to talk.
Murray and the two agents hear Crawford begin to speak. Beginning to sweat, Crawford swears to an unseen Malcolm that he isn't squealing. A few seconds later Crawford combusts in violent flames. Gray stares in horror as the vision of a baby similarly engulfed in flames fills her mind's eye. As Murray tries to extinguish Crawford's flames, agents Kearse and Gray converse. Gray realizes that Malcolm is a pyrokinetic and Kearse theorizes that the "anonymous call" Murray received wasn't anonymous. Deciding to say nothing to Murray, the two leave to pick up the search warrant.
It is now night at the City on the Hill. The two agents find the front gate open and unmanned by security. The two move around the back and enter from the pool area. Inside, the only lit room they find a room full of guns, similar to Alex Clowe's hate group. Kearse says that he doesn't believe it to be a mutant-hating group. Instead, Kearse theorizes that Malcolm and his friends are a under ground mutant militia and the people they want dead is them. Next, Kearse finds and points out plans for a nation-wide strike in concert with other groups, but asks who is handling the organization. Bringing the situation back to reality, Gray tells Kearse that this is too easy; they were meant to find this material. She asks Kearse if it is possible that instead of protecting Malcolm, Whitman was trying to bait them into suspecting him?
Kearse and Gray are knocked down by a wall of flame. Looking toward the flames' source they see Malcolm surrounded by fire. Malcolm tells the two that it was far more likely that his father wished for them to come and kill him instead. Admiring his father's plan, Malcolm points out that he couldn't turn him in (as all of his pansy-ass liberal friends would be outraged) but government agents storming his property with guns blazing... that is genius. Pinning the agents to the wall with his flames, Malcolm tells them that it will take more than them to stop him. Also, while Billy's use of the liver to appear to be a mutant to infiltrate his group was clever, it will take more than that to get past the new Malcolm X. He also laughs that it is a shame that neither Dean nor their mole lived long enough to spill their guts. Resolute, Malcolm picks up one of the M-16s and points it at Agent Gray's head.
Suddenly a screeching sound fills the air, causing Malcolm and Agents Kearse and Gray to fall to the floor. A redheaded white chick, clad in an X adorned jacked and accompanied by her similarly dressed man in a thin visor, speaks to Agent Kearse telepathically. She tells him to sleep, despite his violent objections to her intrusion. An eternity or only a few seconds later, Kearse is back on his feet trying to remember what just happened and why can't her remember?
Later, Kearse sits in Director Kendall Green's office and watches Sterling Whitman on television decry his son's arrest. Incredulous, he declares the charges against his son ridiculous and unfounded. Turning off the television, Green thinks aloud. No one strings a guy to the Hollywood sign for no reason. They do it to send a message. But what message? Green informs Kearse that like he was, Malcolm's memory was wiped clean. Green then asks Kearse about the reported weapons that were not found in the pool house. Adamantly, Kearse says that they were there, but someone must have taken them. Going further, Kearse tells Green that someone is going to great lengths to suppress the truth. Seeing his agent's agitation, Green order s Kearse to go home and begin his two weeks medical leave early. When he comes back, they will start anew.
At a medical center in Crystal City, Virginia Catherine Gray completes her exam. The doctor informs he that from the looks of the ultrasound the fetus looks fine. Somberly she asks if the X-factor prenatal screening showed anything. The doctor replies that it is still too early. Gray thanks the doctor and after putting on her coat, leaves.
Later Kearse returns to his home in Baltimore. Recalling his wife's statement that their son made something for him, Kearse looks on the kitchem table and finds a child's drawing. In crayon, a scene is depicted of a man with a police's star on his chest and an inhuman faced man lying on the ground with green blood pouring from his chest. The inhuman faced man is accompanied by the label "mutant". The man with the star on his chest is labeled simply "my dad". Looking off into the darkened room of his home, Agent Kearse silently broods.