Gwen and Owen pursue a Weevil into a building. While exploring, they find a dead man.
Ianto is working the front desk when a woman comes in and shows him her ID. He hastily ushers her through the secret doorway. Below, Jack and the others are examining the corpse, with an ID belonging to a Meredith Roberts. Ianto calls down to inform Jack that his VIP has arrived. He goes to greet... Dr. Martha Jones. She hugs Jack, who does the introductions. She tells Owen she's there to complete the post mortem and Jack explains she's from UNIT. Martha goes to work and notes there was a statistically significant increase of corpses found in South Wales. They fit a pattern of puncture marks in the eyeball and ammonium hydroxide in the bloodstream.
They check the NHS records and discover that the information has been wiped, supposedly due to a computer crash. Martha notes that an accidental crash wouldn't wipe the data they're looking for so effectively. Tosh starts probing the systems. As they wait, Jack and Martha chat about the Doctor and she admits she misses him occasionally, but she has plenty to keep her occupied. Jack suggests she should have called her but Martha says UNIT came looking for her on the Doctor's recommendation. He takes her on the tour of the Hub and Gwen asks her about Jack. Martha admits that it was intense but she clarifies she doesn't mean sexually. She notices an instrument that Owen speculates is a "singularity scalpel." He demonstrates how it can vaporize an object inside of another one without damaging the outside object. He misses and almost hits Ianto. Ianto informs them there's been another attack but the victim survived and is in the hospital, and her medical records have been wiped just like the others.
Martha and the Torchwood team talk to the woman, Marie, who is unable to identify the attacker. She explains that she chased the man off before he could finish. Martha takes blood samples and goes back to the Hub, where she and Owen analyze the blood and he asks about Jack. She ducks his questions and then wonders why the killer uses ammonium hydroxide. They realize the killer is trying to eliminate evidence of their medical condition in the victims' bloodstreams. Gwen and Ianto pursue the criminal investigation while Tosh tries to recover the computer data and Owen and Martha pursue the medical evidence.
The police report another victim and Ianto and Gwen go to the park to investigate the site and the corpse, a student named Barry Leonard. Back at the Hub, Martha realizes the attacks are more like assassinations, She assures Gwen they'll find out something. Ianto informs them that Marie has had a seizure. They notify Owen, who has found an unidentifiable substance in her blood that appears to be a parasitic infection. Owen notes that she's entirely normal, making her abnormal.
Owen and Martha go to the hospital and ask Marie if she knows what's been happening to her. Meanwhile, Ianto and Gwen talk to Barry's boyfriend Mike, who says that Barry had diabetes but was cured. Ianto notes that it's impossible, but Mike says that Barry stopped taking his insulin and then started flashing some cash about. He notifies Owen, who asks Marie if she's had a serious medical condition. Marie confirms that she had HIV but was cured through the use of a drug named Reset. She says she got it from the Pharm, a medical research laboratory. They gave it to her and paid her a lot of money to keep quiet. Marie collapses and then dies, and a swarm of insect-like creatures fly out of her mouth. Owen declares a medical emergency and they take protective measures, but the insects die in a matter of seconds.
Back at the Hub, Owen analyzes one of the dead creatures and concludes it was incubating inside of Marie's body. They analyze the Reset drug in Marie's body and determine that it eliminates any harmful bacterias, toxins, and mutant cells in the human body. The parasite needs a healthy host and is incorporated into the Reset pills. Various pharmaceutical companies involved in cutting-edge technology own Pharm, and have the clearance necessary to eliminate the computer records. The Institute Director is Dr Aaron Copley, a respected research scientist who came to the UK to set up Pharm.
Jack and Owen go to see Copley and notice that the guards are armed. They're allowed in but Copley denies knowing any of the victims. Jack shows him photos of the victims and explains an alien parasite was involved. Owen tries a more diplomatic approach but Copley denies knowing anything about Reset. Jack accuses him of lying and Copley refuses to let them access the top-security areas. When Jack insists, Copley warns that the company has complete government backing and has his guards escort them out. As they leave, Jack uses his wrist unit to scan the facility and confirm there are alien life forms inside.
Back at the Hub, Tosh warns that she can't access the Pharm systems and they'll soon realize what she's doing if she continues. They discover that Pharm is looking for volunteers and Martha says as a medic, she's the logical choice. Jack initially refuses but Martha notes that she's been in far worse places. He reluctantly agrees. but in private tells Owen that he's rely on Martha if the world was ending. Ianto reviews the building layout with Martha and concludes that a high-security building in the back is where the alien life forms are located. He tells her to be careful until she gets inside, and then close down the firewalls. Martha then asks if Ianto and Jack are an item and he confirms that they are. They provide her with fake ID and contact lenses that let them see what she sees from a distance, and let the team text back to her.
Martha goes in as a volunteer who needs the cash and the doctor in charge, Plummer, asks if she's been to foreign lands. She hedges her answers and is introduced to Copley. They tell her to get close to Copley. When he prepares to dismiss her, They tell her not to lose him and she confesses that she had a hepatitis infection. Copley admits they can use a subject with hepatitis and invites her to stay for clinical trials. He assures her they won't proceed without her informed consent.
As they wait through the night, Tosh comments to Owen that he and Martha seem to be a natural match. He figures that Jack would be jealous if he got together with Martha. He then brings up the pool tournament Tosh invited him to once, and she admits that she was trying to ask him out on a date. Owen admits he had no idea and wonders if she still wants to do that. Tosh says she does and Owen agrees. She's suspicious but Owen says that he's being honest. However, he's not going to stop flirting.
Martha waits in her room until everything is quiet, and then goes out to find the administration office and the computers. She gets there and Tosh sends a signal through the lenses to get the security code for the lock. Two guards arrive and Martha gets inside just in time to avoid detection. Tosh gets Martha to provide remote control of the computer and finds the information on the alien parasite, codenamed "Mayfly." Jack tells Martha to get out but the security alarms go off and notify personnel that there's an alien creature on the loose. Martha slips out a window and heads back to her quarters.
Gwen accesses the personnel files and finds a list of all the victims. Billy Davis, a designated hitman working for the Pharm, marks each one for termination. There is one additional name on the list, Elin Morgan, whose name hasn't come up yet as a victim. Jack sends Gwen and Ianto to bring her in.
Martha gets to a security gate and slips through behind a security patrol. However, the creature comes up behind her and there's a radiation surge. Torchwood loses the signal and Martha is forced to take out the contact lenses. She finds herself face-to-face with a giant flying version of the Mayfly parasite. It comes after her but flees as a security team arrives. The team knocks out Martha with a tranquilizer dart.
Owen is worried that Martha is in trouble but Jack says that she can handle herself. Owen isn't so sure.
Gwen and Ianto head for Elin's address and track Billy's GPS signal to learn he's already there. The hitman breaks into Elin's flat, drugs her unconscious, and then prepares to inject the syringe into her eyeball. Ianto and Gwen arrive just in time to stun him and suggest that they use him to get into the Pharm facility.
Copley talks to a captive Martha and tells her that Jack has treated her in an irresponsible manner. He explains that Torchwood isn't a concern and in fact they want Martha, who has unique biological readings.
Jack threatens to unleash a Weevil on Billy unless he tells them what they want to know. He breaks and tells them he was sent to eliminate the clinical test subjects.
Copley explains that Martha's cells have mutated due to temporal radiation. They've dealt with aliens, but nothing as exotic as Martha: a human being who has travelled through time and space. Copley wonders what she's seen out there but Martha denies everything. He explains that Reset is still imperfect and wants to see how her lymphocytes interact with the Reset drug.
As Jack prepares to have Billy take them into the Pharm, the hitman convulses and starts vomiting blood. They realize he has a parasite in him and Owen starts to use the singularity scalpel. The creature bursts free and then dies, and they realize Billy breathed in the larva from one of his victims.
Martha's system reacts with the Mayfly larva.
Tosh comes up with a way to use Billy's corpse. They tape its hands to the steering wheel of his vehicle and remote-drive it to the gate. Once the guards let them in, the team enters the facility, Jack and Owen break into the lab and Copley explains that Martha managed to survive the incubation stage. The larva consume each other and only the strongest one survives, and Copley admits he has no idea how to cure her.
Gwen, Ianto, and Tosh find the facility where the Mayflies are being kept. Plummer explains that they harvest aliens for medical purposes, and have a Weevil that provides them with pesticides and a chemical defoliant. She shows them the Mayfly, their primary product.
The surviving larva begins to grow within Martha and Jack tells Tosh to shutdown the facility. He accuses Copley of conducting torture but the doctor defends his actions, insisting they were going to die anyway. Jack explains that he's going to crash their systems and wipe all of their computer records, and then set off alarms that will flood the facility with inert gas. Copley warns that it will kill the aliens but Jack insists that he's putting them out of their misery. Martha goes into convulsions and Jack goes to hold her down while Copley escapes. Owen uses the singularity scalpel and removes the Mayfly just in time. She flatlines for a moment and then revives. The two men get her out of the facility.
As they leave, Owen flirts with Martha, who explains that she has a boyfriend. The team takes the rest of the staff into custody and Tosh shuts down the facility. Copley arrives with a gun and accuses them of ruining everything he's worked for. Owen tries to appeal to him as a rational man but Copley shoots him dead. Jack shoots Copley in the head, killing him. Martha tries to keep Owen alive but they can only watch in horror as he dies.