Samantha Jones has been having a really weird day. A man shows up at her door, calling himself the Doctor and claiming they've met. He insists that she's traveled with him in his space-time ship and seen the universe. He also insists that she's supposed to be blonde.
This is the Sam that should have been. It turns out the paradoxical dark-haired girl from blonde Sam's dreams has finally caught up to her, as has reality. Dark Sam is the real one. The only Sam Jones there is. The Doctor tries to talk to her, but sensing that something isn't right, she ignores him. After Sam leaves this nutter behind, she's ambushed by young kid with a knife and no shadow. The Doctor saves her but is injured himself, and entreats Sam to trust him, which she reluctantly does. They meet Fitz in San Francisco, 2002, to examine a temporal rift that's causing the city all manner of trouble.
They are abducted and tagged with tracking devices designed to tap into the Doctor's biodata, which for some reason is spread out and tangled up all across the city. The man who is watching them is an unnaturalist, or hunter of exotic (read: alien) flora and fauna. The unnaturalist is interested in a kraken that has emerged from a higher dimension, attracted to the rift as a source of food. The thing has been sleeping in the San Francisco Bay for a few days and its immense size poses threat to the entire city. Fitz meets with a hippie woman who helps him investigate ley lines running through the city, converging on the places where the Doctor's biodata is the most tangled. They discover that the rift is a actually a scar in space-time caused by the opening of the Eye of Harmony in San Fran when the Doctor regenerated, and that the only thing stopping the kraken from rolling right over the city and crushing it to swallow the scar is the TARDIS, who threw herself into the dimensional anomaly to act like an impromptu sealant, containing enough dimensions of her own to temporarily mask the rift's existence. Problem is, the TARDIS is in agony, being pulled apart by the forces of the rift, and the only way to permanently seal the rift would be to allow her collapse into it completely, an act which would destroy her. With San Francisco behaving even more oddly than usual, the Doctor and Fitz must convince this alternate Sam to help them close the scar before the city is obliterated.
Tropes present in Unnatural History include:
- Big Damn Kiss: Between Sam and the Doctor and Sam and Fitz.
- City of Weirdos: San Francisco is portrayed like this even before the rift opens up. It's a testament to the city that aliens and unicorns are wandering around mugging citizens for chocolate bars and no one even notices.
- Curse Cut Short: A Faction Paradox member taunts the Doctor with a parody of a Gallifreyan rhyme:"Sing the past to me, 'cause I'm the one who wrote the song
I made it up next week so all the words will come out wrong
The past won't keep you warm tonight, the future's blown to bits,
And everything that you believe is really full of —"
The door slammed behind him.
- Doing In the Wizard: Griffin's MO is an in-universe form of this. He can't abide "impossible" creatures, so he breaks them down enough so they can be properly cataloged.
- Eldritch Abomination: The kraken is described this way. It's an extra-dimensional leviathan attracted to Earth by the rift, so impossibly huge that its sheer presence in San Francisco Bay poses a threat to the city.
- Glad-to-Be-Alive Sex: Fitz and Sam, after witnessing a particularly gruesome murder.
- Heroic Sacrifice: Dark Sam throws herself into the space-time scar to bring back blonde Sam, the only one who can save the Doctor; by doing so, she comes into contact with the Doctor's biodata and her own is transformed, creating blonde Sam for the first time. As the Faction would say, a neat little paradox.
- In Spite of a Nail: The Wild Hunt changes the little details of Sam's life, but she's still Samantha Jones... until a real, significant change occurs that leaves her a wasted addict suffering from withdrawal and absolutely wretched.
- Newspaper-Thin Disguise: Played with twice. In the first instance, Fitz doesn't seem to be attempting to hide, but came across as shady nonetheless. The second time he does it, this time actually trying to camouflage himself, he realizes that the newspaper is in Chinese, and, unluckily for him, while he does speak Chinese, he can't read it.
- Temporal Paradox: The entire plot, and in fact Sam's entire presence in the series, hinges on one.