Things are certainly starting to heat up again. We start this episode with a young buy dying of Cancer, whose parents refuse to allow treatment on due to their religion, so instead they pray for his recovery.
Funnily enough, overnight he makes a full recovery from terminal Cancer. Clues about this are left on Scully’s doorstep and Mulder gets an anonymous email about this miracle (we also note Scully dispute the claim he can recover from a terminal illness, even though it happened to her!). On speaking to the kid, Scully heads home only to find Smoking man sitting in her car.
He explains he healed the child, and that he is dying. He offers Scully a chance to learn of the secrets that cured the child, and her own Crazy Cancer, since now he’s dying, he wants to do good in the world. Scully instantly tells him to sod off in her own words, yet he leaves his business card – just a phone number.
After a little consideration, she traces the number and heads over to the office – it’s like they are expecting her. She heads to the third floor to find and office titled ‘CGB Spender’. On entering a man in a long coat and blonde hair watches her enter. She finds smoking man, who thanks her for coming and goes on to explain his reasons a little further. He explains that his life work has been destroyed, and his legacy no longer stands – since he doesn’t want to go unnoticed, he’d like to do one more good thing for the world – and can give Scully information about the cure to everything plaguing mankind. Scully is at first reluctant, thinking he’s only after it for his own selfish reasons – yet she agrees. After all, being a doctor, how can she refuse.
Smoking man informs her they’ll need to take a few days away. So she calls Mulder to tell him of a family emergency and she’ll be away. As Scully gets ready, we get a close up of her bra as she attaches a wire to herself, and they begin their trip. The strange blonde guy with the long coat follows. Mulder’s getting a little suspicious and speaks to Skinner, who receives a call from her stating she’s fine. He heads over to her apartment to look for clues, but before he even gets in, a man in Scully’s apartment building recalls her driver smoking like a chimney, so he calls in the Lone Gunmen to do their own investigation into where she may be.
Meanwhile, with nothing but driving time ahead, Smoking man explains his reasons for choosing Scully. Stating he’s always had an affection for her, and although she’d happily risk her life for Mulder, she could never love him – perhaps she’s attracted to powerful men, but is afraid of their power. This new found side of him is challenged by Scully when he lights up another smoke. He throws it out the window, stating he’s been meaning to quit. As they stop at a gas station, she attempts to mail the tape she’s secretly been recording in the car off to Mulder – however it’s prevented from reaching him by blonde guy.
Scully, still not 100% sure smoking man is being genuine gets a little more proof when they stop at an old ladies house. Smoking man informs Scully that the woman who looks in her 60’s is in fact 118. Thanks to him. She hugs Smoking man, and they share some freshly baked bread. Finally, they reach their destination. Mulder however has discovered something not very comforting and tells Skinner. They find that someone has been intercepting her emails and posing as Scully in an online chat with someone only known as Cobra, who works for the DOD on a secret shadow project researching advanced technology.
Cobra thinks he’s talking to Scully – and wants to give away the secrets of curing Cancer to her since he’s sure it can be trusted with her. Scully has no way of knowing this but heads out to dinner with Smoking man where he promises to meet this man and exchange the information. They get nothing but a note telling them where the next meeting point is. We also briefly see Smoking man talking with blonde guy. Cobra wants to meet Scully in the middle of a lake, so out she sets.
He gives her the disc of information and she asks where he got it. Suddenly Cobra knows he’s not been speaking to Scully and is shot by a sniper – blonde guy, who then attempts to take Scully’s life, but is stopped when Smoking man kills him. He’s back just in time to see Scully return, slightly angry she was shot at. She hands him the disc, to which he returns it – stating it’s hers. Finally she returns to Mulder’s apartment to read the disc. It’s blank! Mulder explains to Scully she was used to obtain the disc. Smoking man posed as her to gain Cobra’s trust – he then got Scully to get the disc, killed everyone off except Scully (were not quite sure why she was allowed to live).
They return to his offices only to find them empty, and Smoking man has the disc in his possession. He now has the ability to cure himself, save anyone… or destroy anyone. Scully was convinced he was telling the truth, and tells Mulder that for a second, she saw real compassion in him – like he’s slowly giving up.
The end of the episode shows Smoking man holding the disc, then throwing it into the lake and lighting up a new cigarette.