While Weevil hunting one evening, Tosh and Owen come across the corpse of a man who died under mysterious circumstances. Jack calls in Martha Jones, now a doctor working at UNIT, to help with the investigation.
Martha is welcomed warmly by Torchwood. She catches up with Jack regarding the events of the lost year and tells him that her family is gradually recovering from the trauma. She also befriends Gwen, asks Ianto what Jack is like in bed ("innovative... bordering on the avant-garde"), virtually ignores Tosh and flirts with Owen. Jack and Martha once again share a moment about the Doctor apparently being oblivious to them and speculate that The Doctor got Martha the U.N.I.T job she has as an apology.
Tosh finally — finally — asks Owen out on a date. He's fine with it, though not exactly enthusiastic.
It turns out there is a series of deaths which only have one thing in common: death by hypodermic needle in the eye and a connection to a mysterious pharmaceutical company aptly named the Pharm. The patients miraculously recover from incurable illnesses, only to die from some kind of parasite soon after. Martha volunteers to investigate undercover as a test subject.
The team discovers that the Pharm has been using alien mosquitoes as guinea pigs to manufacture miracle cures. Martha is tortured and implanted with an alien chestburster. Owen saves her life just in time, but he gets shot by Dr. Copley. Jack immediately puts a bullet in Copley's head, but Owen is lying there on the pavement, critically bleeding out before his horrified teammates. Martha can't save him from his injury, and Owen dies. Heavily saddened, Jack must come to terms that he's lost another friend.
Tropes:
- Big Brother Instinct: Jack is very resistant to putting Martha in danger and becomes furious when she gets captured and almost dies at the hands of Dr. Copley.
- Big Creepy-Crawlies: The Mayfly are an alien race that resembles mayflies. They're also already a foot long when they burst from their hosts' bodies and can grow up to several metres as an adult.
- Blood from the Mouth: It's a big sign that the bullet wound that Owen has received from Dr. Copley is fatal when he bleeds from the mouth.
- Boom, Headshot!: Once Owen is shot by Dr. Copley, Jack retaliates by killing Copley with a clean shot through the head.
- Call-Back:
- Martha mentions this isn't the first time she's had to be invisible.
- There are also a bunch of hints to the Doctor by Martha and Jack.
- Continuity Nod:
- The Eye Drive contact lenses later play a key role in all of season 3.
- Subtle references to the Doctor and the Master galore!
- Crossover: Martha shows up and remains for three whole episodes!
- Everyone Has Standards: Jack will flirt with literally anything that moves, but not Martha. This isn't because he doesn't find her attractive - he does - but because, after everything they've been through together, Martha has earned his respect and deserves better.
- I'll Take That as a Compliment: Ianto declares Tosh to be warped on the inside when she presents him with an idea on how to get into the Pharm with the dead assassin propped up in the driver's seat. After a Beat, she takes it in stride.
- Mercy Kill: Jack opts to do this for the parasites, as the containment modules they were in were inhumane. He points out that they're already dying thanks to being used for the Reset drug; Jack killing them puts them out of their inhumane farming misery.
- Mood Whiplash: The episode starts out lighthearted and nostalgic, but ends with an actual death of one of the team.
- Mythology Gag: Martha's infiltration alias is "Samantha Jones", which was the name of the Eighth Doctor's first ongoing companion in the prose Eighth Doctor Adventures.
- Predatory Big Pharma: Torchwood investigates a biomedical research facility called the Pharm, who are secretly abducting and experimenting on aliens from the Rift to fuel their research and have caused several deaths, by using "volunteers" as hosts for a drug that contained a deadly alien parasite as well as hiring an assassin to silence their volunteers. Captain Jack is revolted by the Pharm's mistreatment of the aliens, saying there's a fine line between policing hostile aliens and forcibly using them as lab rats without ethics, so he uses cyberterrorism to wipe out the company and Mercy Kill their test subjects.
- Really Gets Around: Discussed by Gwen and Martha in regards to Jack. They confirm that neither of them has slept with him and joke that they must be the only two in the world.
- Secret-Keeper: Ianto apparently knows who Martha is, implying Jack has told him, at least, what happened in that absent year.
- Special Guest: Freema Agyeman as Martha Jones.
- That Came Out Wrong: Martha tells Gwen that she and Jack were only together a few days, but it was very intense. She then has to clarify that she didn't mean they were in a relationship.
- Touched by Vorlons: Martha is better able to survive the Mayfly gestation process because exposure to Artron energy in the space-time vortex has caused her immune system to mutate. Which finally, after more than 40 years of Doctor Who, explains why companions aren't all the time falling prey to alien and extemporal diseases.
- Wham Episode: Owen is killed.
- Yaoi Fangirl: Martha seems quite pleased about Jack and Ianto's "dabbling".
