Liz receives a new grant in San Diego, allowing her to leave town. Despite learning that his ancestor was killed by an alien in 1947, Kyle refuses to assist Project Shepherd. Max and his partner Jenna identify a local, Wyatt Long, as the man who shot Liz, and embarrass him in a shooting contest. Isobel and Michael try to intimidate Liz, but Max defends her. Kyle agrees to help Liz find her sister's hidden autopsy report, which reveals that she did not die in an accident. At the same time, she learns from her psychic bond that Max was with Rosa on the night she died. Wyatt and his friends assault Liz's father; Max beats Wyatt and nearly kills him with his abilities before his siblings intervene. Conflicted by Max's actions saving her father, Liz asks him to tell her when he last saw Rosa, and he lies. Michael strikes up a relationship with Alex Manes, a veteran working near his trailer, while Max has sex with Jenna at her house. Liz decides to stay in Roswell, telling Kyle that she intends to bring her sister's murderer to justice, even if it is Max.

Under the guise of treating him, Liz tries to scientifically determine if Max killed Rosa. Isobel and Michael, fearing the consequences of Liz learning too much, concoct a plan to drive her away. Maria gives Liz a secret map written by Rosa that leads them to a clue suggesting that she had a secret relationship. Max asks Jenna out on a date. After Kyle sees an injury on Liz caused by Max's abilities, he secretly copies his father's research on aliens for Project Shepherd. Isobel telepathically probes Liz's mind, but is unable to compel her to leave after seeing images of Rosa. Liz confesses to Maria that she nearly married, but ultimately chose to leave her fiance. She then discovers a love letter from Max to her sister, but he reveals that the letter was actually meant for her. Sheriff Valenti warns her son not to trust Project Shepherd. Max swears that he did not kill Rosa, and begs Liz to leave the past behind. Kyle turns over the copies to Project Shepherd, but makes it clear he will provide no further assistance. Max suffers a nervous breakdown and unleashes the full extent of his powers, triggering a town-wide blackout.

A flashback to 2008 shows Rosa warning Liz not to pursue a relationship with Kyle. In the present, Max and his siblings discuss how to handle Liz; Isobel offers to use her powers again and leaves with Michael to strengthen them. Arturo goes into cardiac arrest, and winds up hospitalized, during which Kyle offers Liz a bioengineering job. Max offers to make things up to Jenna. Isobel tests her powers, learning from Maria that she blames her for Rosa's death before seizing up. Rosa's old boyfriend Frederico gives Liz her old backpack, including a letter with distinctive handwriting. With the hospital's failing power putting its patients in danger, Max fixes the main power unit, leaving behind a scorch mark that Jenna notices. Liz confronts Kyle, accusing his father of having an affair with Rosa; Kyle, in turn, reveals his father knew about aliens. When Max asks Liz how does she feel about him, she reveals being terrified of him, so Max decides to end things between them for good. Jesse, Alex's father and a member of Project Shepherd, presses Jenna for access to Sheriff Valenti's files. Michael tells Max and Isobel that he will confess to Rosa's murder to protect them.

Isobel disappears, so Max and Michael set out to find her. Liz finds a recording from the night her sister died with a local documentarian, Grant Green, saying that he saw "floating people", but when she confronts him, he runs off. Kyle and Alex uncover a vault belonging to the late Jim Valenti that he used to keep Rosa safe while he helped her detox from her addiction. Liz breaks into Green's storehouse and confronts him again; he shows her a tape of what he saw. Isobel is rescued, but accidentally admits that she used her powers on Liz years earlier to send her away after Rosa's death. Kyle discovers that, rather than take advantage of her, Jim was, in fact, Rosa's father, which explains why he went to such lengths to shield her. Max forces Isobel to track down Liz, who is captured and interrogated by Wyatt, who has been sent to silence Green. She escapes, and runs into Max, who shoots Wyatt. Noah kicks Isobel out after she refuses to explain why she left. Alex finds a piece of alien husk hidden by Jim. Liz realizes that Max covered up Rosa's death because Isobel killed her.

In 2004, a young Max uses his power for the first time to save Isobel from a rapist. He explains to Liz that the trauma of that night caused Isobel's blackouts. In 2008, at their high-school prom, Liz leaves her date, Kyle, when Alex accuses him of using an anti-gay slur. Isobel grows closer to Rosa, who wants to leave town so she can get clean, and disappears that night, sparking an argument between her brothers and her. Liz and Max go on a trip into the desert, where Max confesses his dream to be a writer. Alex and Michael discover they are attracted to each other, and hook up. Jesse catches them, and breaks Michael's hand. A drunken Rosa drives Max off just before Isobel kidnaps and smothers her in a jealous rage after previously killing two girls who had vandalized Rosa's car before blacking out, which causes her to suffer amnesia. Michael lies and says that he killed the girls, and the siblings stage a car accident to destroy the bodies. A horrified Liz tells Max she never wants to see him again. Isobel tells Michael that she is ready to answer for what she did.

In 1947, Project Shepherd conducts an autopsy of a deceased alien, discovering a strange symbol on its hand, which matches one on Max's back. Max is reinstated as a deputy, but denied permission to return to active duty, and Liz agrees to help Maria with her mentally ill mother Mimi, who believes in the existence of aliens, which she frequently confuses with the plot of Independence Day. Jenna questions Wyatt, who professes ignorance of trying to kill Liz, and witnesses him unconsciously sketching Max's symbol. Mimi gives Alex a vague warning about not ending up like Jim Valenti and his father, and mistakes Liz for Rosa, which she plays along with to gain her trust. This allows her to learn that Isobel confessed to being an alien to Rosa. Max discovers that Liz has been conducting experiments using his DNA to develop a serum that neutralizes alien powers; Isobel, wracked with guilt, agrees to be placed on a temporary psych hold. Max asks Liz to continue working on the serum in the hopes that it might allow his siblings and him to lead normal lives. Jenna gives Max's name to Jesse for further investigation.

Max visits his mother, Ann, for answers about his past. Kyle learns the truth about Rosa's death from Liz, and injects Isobel with the untested serum, which she claims was partly because she influenced him to do so. Alex knocks out his father and questions him about Project Shepherd. Isobel's health begins to deteriorate rapidly; Liz estimates she will be dead by the end of the day. Alex learns from Jesse's files that Michael is an alien. With no other options, Liz turns to alien research conducted by Michael in secret, which leads her to conclude that Isobel can only be saved by using the pods to keep her in suspended animation. Deducing that silver affects the pods, Liz concocts a substance to get Isobel into one of the pods, which she consents to after overhearing Max ranting about how he wishes he loved her less. Alex blackmails his father to shut down Project Shepherd and leave Roswell, accusing him of being blinded by his homophobia. On his way out of town, Jesse runs into Jenna, and tells her to keep an eye on Alex and any other alien phenomena in town. Michael begins to suspect that Max's symbol may be a "beacon" of some kind.

Six weeks after putting Isobel in stasis, Liz and Michael are no closer to a cure. Desperate, Max goes to Texas to meet Arizona, a faith healer he thinks may have alien abilities; Maria tags along hoping that Arizona can heal her mother, only to wind up shattered when Michael exposes Arizona as a fraud. Jenna asks Alex and Kyle about what she thinks is a police coverup concerning several mysterious deaths, and they reveal to her the existence of aliens. Alex subsequently restarts Project Shepherd to track a potential alien serial killer. Max confesses to Liz his guilt over not using his abilities to save more people. Later, he learns from Arizona's mother that a woman with healing powers died on her reservation around the time he arrived on Earth. Noah goes to find Max, and inadvertently discovers the pods. Kyle realizes that his father's death was covered up by Jesse. Alex decides that he wants to connect with Michael, even after realizing that he had sex with Maria. Liz tells Max that all signs point to a fourth alien in Roswell, who may possess knowledge of his home world.

Max and Liz take Isobel out of her pod and inject her with the cure, seemingly taking away her blackouts. Michael shows Alex his plans to build a ship to leave Earth, leaving him emotionally conflicted. Noah is reluctant to take Isobel back, knowing that she is an alien, but eventually accepts her. Sheriff Valenti gives Kyle the rest of his father's letters. Isobel recovers some of her memories of Rosa, and decides to ask Liz for another dose. Maria confesses to having sex with Michael to Alex. A gunman attacks the hospital, and Noah is shot in the shoulder. Max rescues them and finds the shooter, who sets fire to Liz's laboratory; he claims that he does not remember the incident. Alex and Kyle use the piece of husk the former found to decode a secret message left by Jim Valenti, which references Caulfield, an old state prison. Isobel concludes from her memories that she loved Rosa and wanted to protect her, and gets more of the cure from Michael. Liz tells Max that she thinks the killer may have the ability to mentally control people when they black out. Isobel regains her memory of murdering Rosa while under the killer's influence.

As the town prepares for the UFO Emporium reopening gala, Max asks Liz to be his date, but she declines, since she needs to accompany her father. Wyatt informs the police that he saw one of the murder victims with Maria. Liz's stem cell project is relocated to Palo Alto, but she is reluctant to leave her father again. Max and Michael are both abducted and locked in Michael's lab using a powder that neutralizes their powers, which makes them both irritable, until Max admits that he feels angry Michael was not adopted by his parents. In turn, Michael explains his cynical view of humanity and his fury over how Max expects him to act human even when it means hurting the people he loves. The killer drugs Maria, and uses her to steal a fake-cure syringe planted by Liz, who finds and rescues the brothers. Liz tells Max that if he truly loves her, he will not let her run away again. Arturo decides to apply for citizenship. Liz tests a sample of Noah's blood and realizes that he is an alien at the same time that he compels Isobel to kill Max. Jenna saves him, and Liz injects Noah with the serum before Max subdues him.

Liz, Max, and Isobel hold Noah while Max and Isobel question him. Alex, Kyle, and Michael travel to an abandoned prison, Caulfield, to the north. They find aliens imprisoned and tortured for 71 years in the care of Alex's brother. When Michael sets off an alarm while trying to free the prisoners, a timer is initiated and the prison is destroyed, killing all the alien prisoners including Michael's mother. He returns to Roswell and squares off against Max about letting Noah die.

Max wakes up and heals an unconscious and injured Michael. Isobel shows up and Max leaves with her on Noah's tail. Liz is in the diner and Noah shows up. Liz temporarily captures him but he escapes and injures her. Isobel directs Max to Noah but she was under Noah's control the entire time. Noah subdues Max. He takes them to the cave where their pods reside and prepares to place them in the pods as leverage for when the aliens come to take them back. Michael shows up and distracts Noah while Max gets an energy charge from the storm. Max attacks Noah and kills him. The next day Max and Liz hook up, Michael and Isobel find Noah's cave and find Rosa in his pod. They call Max and convince him not to tell Liz. Liz practices her powers, whereas Michael goes to Maria and sings for her indirectly expressing his emotions. In the cave, Max uses his powers to resurrect Rosa. Liz feels he's in trouble and shows up there just to find Rosa alive and an apparently dead Max.

Two weeks later, Max's body is being kept in a pod with his death kept quiet, Rosa is hiding out at his place prior to Liz taking her out of town for a fresh start, and Noah's death has been passed off as a lightning strike. Michael sabotages his relationships with both Alex and Maria. Liz realises Max still has a psychic connection to Rosa: Despite his heart being destroyed, his brain might still be alive. Flint tries to steal Noah's body but is stopped by Liz and Rosa. Liz, Kyle and Michael harvest Noah's heart, which Liz is convinced she can repair and use to revive Max. Isobel realises she is pregnant. Rosa sees Max in a dream, telling her not to let Liz bring him back.

Alex helps Liz and Michael set up a lab in an abandoned government facility. Michael gets into a fight with Wyatt Long when he tears down one of the Missing posters for Mimi. Rosa learns how people in the town really feel about her and is furious with Liz for continuing to protect Max. Kyle and Alex use the video of Manes killing Valenti to blackmail him. Kyle meets Steph, the Dean of Surgery's daughter. Maria organises a female empowerment session that Isobel and her mother attend. Isobel takes some of the alien death serum to try and cause a miscarriage. Michael sets up camp in Maria's parking lot and they kiss. Rosa starts drinking to block out the visions of Max.

In 1947, Manes and Valenti's fathers encounter the survivors of the crash. In the present, Jenna returns to town and finds Mimi in the middle of nowhere, with no memory of the last month. Jenna visits Liz at the lab and finds out what's going on with Max. Isobel sees visions of Max as she continues taking serum to force an abortion. When she miscarries but is too weak to give herself the antidote, Max contacts Rosa who sends Liz to save her. Maria encounters Rosa at the Wild Pony and discovers the truth, leaving her furious with Liz and Michael. Michelle asks Isobel about Noah being restrained before he died but Isobel passes it off as sex games. Michael and Alex view the files of the crash aftermath and discover the aliens' mothers escaped with the pods containing them. In 1947, the two women are helped by a black homesteader.

1947: Bronson, the foreman of the Long ranch, agrees to shelter the two mothers. In the present day, Michael and Alex learn that soldiers led by Alex's great-uncle came there a year later, killed the humans who had helped them and abducted the pair. Liz asks Kyle to help her steal a genome machine from the hospital. In the process, she kisses him to get Steph suspicious, which leaves him uncomfortable. Jenna confronts Manes about Charlotte's whereabouts and he explains she had herself sent to jail because she had been involved in research that could be used to create a bioweapon. Isobel mind-warps Arturo to accept Rosa's return.

Liz, Michael and Isobel discover Max's pod has shorted out. Rosa realises he did it himself, telling them about her dreams. Liz decides she and Kyle will transplant the faulty heart into Max so he can at least live long enough to say goodbye. Isobel uses Rosa to enter a dream state with Max; he believes he absorbed dark energy when he revived Rosa and will want to hurt everyone. Alex and Maria clear the air and he also convinces her to forgive Liz. Michael comes up with an alien pacemaker to keep Max alive and, when it seems he will still die, Rosa demonstrates alien-like abilities to charge the defibrillator and revive him. After three weeks in a coma, Max awakes and he and Isobel face off.

Isobel takes down Max, who is then revived by Michael, but he has no memory of Liz. They go on a first date together horse riding and Liz begins to suspect he is happier without his memories of her. However, they come flooding back after he finds the bullet she was shot with and the couple spend the night together on the roof of the Crashdown before she tells him she loves him. Maria takes Alex to visit Travis, the man who made the boots Mimi had when she was found, but he attacks them with an axe. Michael also arrives and they are saved by Travis' twin brother Trevor, who says Travis was part of a military experiment. Michael, Maria and Alex share a threesome. Isobel meets Kyle at a gay bar and tries to seduce him but ends up hooking up with the bargirl, Blaire, instead. Alex finds Steph being operated on at the hospital.

Isobel tries to train Rosa to use her powers. Liz and Rosa's mother Helena arrives; Arturo wants her to sign her half of the diner over to Liz in order for her to sponsor his citizenship but she insists on a family meal with Liz, Arturo and Max first. She seems to want to make amends but turns out to be stealing. Arturo gives her his mother's ring in exchange for the contract and Max later retrieves it by threatening to reveal her past to her politician boyfriend. Rosa accidentally torches Helena's car after stealing some pills from it. Michael and Kyle look into Maria when she starts receiving visions and discover her grandmother was part of an experiment to try and give people alien powers. Maria uses her vision to save Kyle from being run over. Kyle and Steph kiss. Max realises Jenna is missing and decides to look for her.

Liz and Isobel try to help Rosa pose as a distant cousin and she befriends a girl, Iris. Max and Liz meet with Charlie, who has come to town looking for Jenna. Max quizzes Manes, who points them towards a black ops group, Deep Sky. Max and Charlie rescue Jenna from a sealed container after which Charlie disappears again. Alex goes paintballing with Forrest but is still uncomfortable about publicly dating him. Michael realises Maria's necklace contains alien pollen that stops her using her powers, preventing her brain degradation. Liz finds Rosa collapsed from an overdose, having imagined Iris. She gives her Maria's necklace and checks her into rehab. Maria and Isobel share a vision of Isobel's mother with Walt, and Michael realises he is Sanders. Max finds Charlie shortly before they come under attack.

Kyle takes Steph on a date to the diner but she leaves after he admits he knows she's dying. Liz tells him she's hoping to use the aliens' DNA to find a universal vaccine. Michelle arrests Max over the disappearances of Mimi, Jenna and Charlie. Isobel is unable to mind-warp her because Kyle laced her perfume with the yellow pollen, so Kyle helps Max convince her he was having a heart transplant at the time. Sanders gives Michael and Isobel his account of the farm raid but Alex becomes convinced Tripp was actually helping the aliens. He, Liz and Isobel find a photo left for Tripp at the diner showing Isobel's mother Louise as an older woman.

In 1948, Tripp takes the injured Louise to a friend, Harrison, on a native reservation. In the present, Alex takes Max, Michael, Isobel and Maria to the reservation, where his mother came from and his brother Gregory lives. He shows them Louise's grave, where Michael finds one of the alien flowers for Maria. Max and Isobel are able to enter the dreams of the aged and dying Harrison and learn Louise had a daughter and Max wasn't her child. The group deduce the baby was Maria's grandmother. Arturo is arrested by immigration police on a trip to the hospital. Liz and Jenna learn Liz was refused as sponsor because of her vandalism charge, and Liz has Diego arrange for his senator mother to have Arturo released. Diego discovers evidence Jenna was given a military memory erasure drug. Alex forces Michael to give him the piece of alien technology he found but is then attacked and abducted. Max has a flashback of Louise fighting someone to rescue him.

Liz has a dream of Diego proposing to her. He spends the day helping her out at Crashdown and tries to get her to accept funding from his company, Genoryx. Kyle is suspended from work suspected of stealing hospital resources and helps Max investigate Jenna's disappearance. Steph manages to get him reinstated. Michael discovers Alex is missing and that Manes originally took him before he was taken again by Flint. Isobel visits Rosa in rehab and they discover Helena has also disappeared. Liz and Rosa realise Helena and Flint are working together. Flint takes Michael to Helena, who wants him to build a bomb.

Liz, Maria and Isobel deduce that Mimi was with Helena when she disappeared. Helena forces Michael and Charlie to construct an atomiser which will release a toxin that targets aliens. Michael realises Helena is swapping it for one that will kill Manes and his family, in revenge for Jim's murder, so leaves Alex behind as a prisoner. Max and Jenna check out a storage facility Kyle found together and Max admits he is using the antidote to restore his memories of his old life. Flint gets the real atomiser from Charlie and leaves her chained up in a burning building. Liz realises Manes intends to cause a disaster and blame aliens so he will look like a hero for killing them: Graham Green has an alien artefact, supposedly given to him by Max, that will explode if ignited by the CrashCon fireworks display. Flint releases the anti-alien atomiser at the event; Maria gets it to safety but is infected in the process. Alex, Gregory and Michael all confront Manes together, while Max uses his powers to try to kill Flint before collapsing. Rosa wants Liz to help defuse the bomb but she tries to revive Max instead.

Liz and Isobel manage to stop the bomb exploding while Rosa revives Max. Jenna gets Maria to the hospital (where she is saved by Liz's serum), Charlie is rescued by Helena and Gregory kills Manes when he tries to shoot Michael. Diego introduces Liz to Doctor Margot Meyerson who offers her a job in California. Max destroys Liz's laboratory to stop Diego from seeing it. Liz visits Steph and, soon after, Kyle finds she has miraculously recovered. Michael and Alex find Tripp's body buried under the Manes shed and that he left Mimi a journal, which reveals a stowaway, Mr. Jones, caused the ship to crash and attacked the soldiers, prompting the massacre. Alex kisses Forrest after singing at open mike night. Max, Isobel and Michael find a pod containing Mr. Jones, who resembles Max.