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The storm. It's coming.
Taking place about six months after the The Movie, the Serenity crew is strapped for cash and takes on the ridiculous job of hunting down an alien. Meanwhile, after the events of The Runaway Bride, the Doctor decides to go someplace completely new, and finds himself having to convince Mal to take him on as a passenger. So long as their ship has enough room for a blue storage shed..
- Alien Blood: The Doctor's blood is a paler shade of red than a human's.
Simon: His blood is the wrong color!
- Alien Invasion: Right after the colonies left, Earth was hit with a bunch of these. The Doctor claims it's probably why the colonies have been cut off for so long.
- Always Lawful Good: Mokshar. Their bodies are somehow evolutionarily programmed to stop working properly if they break their own Actual Pacifist-based religious laws. The Big Bad, however, is pissed off enough by the Time War that he manages to subvert this... initially.
- Back From the Dead: At one point, Mal dies, but comes back to life.
- Bad Liar: The Doctor laments his inability to lie convincingly in this regeneration several times.
- Balancing Death's Books
- Bar Brawl: Early on, the Doctor wears his usual attire (a brown coat) into an Alliance friendly bar. Much to his confusion, he is quickly punched out a window.
- Badass Boast:
"Yes, I think war is a fool's game. Yes, I believe life — all life — is precious. But tell me something, Vharaj — did you ever listen to my enemies' tales of me? If you did, it's obvious you weren't paying attention. The Daleks do not have emotion, Vharaj. They don't know fear. But do you know what they called me? Ka Faraq Gatri. It means Destroyer of Worlds. I am the Bringer of Darkness, Vharaj. The Oncoming Storm. I've watched worlds and galaxies fall, and rise, and fall again. I fought the Vampires at the dawn of Creation, and I may yet witness the end of the Universe. I brought about the destruction of my own race, the deaths of my children, my grandchildren, my siblings, my friends, all in the name of peace, to save this Universe. So you tell me, Vharaj: what do you think I am capable of?"
- Beware the Nice Ones: The bad guy failed to do this. He pays for it.
- Big Damn Heroes: It's Firefly and Doctor Who. Of course there's Big Damn Heroes.
- Bizarre Alien Biology: The author mentions a couple of the odd quirks of Time Lord biology that were mentioned in the sereis proper, including some that were mentioned only once. These include:
- Two hearts.
- Very low body temperature
- Blood being a different shade of red from a human's
- Respiratory bypass when badly winded; mentioned by name in the 4th Doctor serial "The Robots of Death" and was a plot point in the Fifth Doctor's last serial.
- A violent aspirin allergy, from one of the Third Doctor's serials.
- Bring News Back: Zeke, the leader of a town the crew saves from a few Reavers sends them a message that the village has been wiped out by an army of them before dying himself. The crew is not happy.
- Chekhov's Gun: Partway through the story, the Doctor needs to wash his coat, so he empties his (very very large) pockets. Among the many things he excavates from them are the last of the Christmas ornament explosives from The Runaway Bride. These get used in the escape from Renier Enterprises.
- The Chessmaster: The Doctor muses about 'getting the pawns in place' when enacting his Batman Gambit.
- Closest Thing We Got: The Doctor ends up needing Simon to operate on him when he gets shot. Not that Simon knows anything about Time Lord biology...
- Combat Pragmatist: Mal does try to shoot him. It doesn't work.
- Common Crossover: Both series are beloved sci-fi television shows with a nice dose of cynicism, feature characters who travel through space with no destination and are renegades/outcasts in society (though with the nature of Doctor Who, it's easy to dump him in just about any series).
- Death Equals Redemption: The villain dies to save the Doctor and Mal's lives.
- Dying Declaration of Love: While escaping the enemy stronghold, Mal does this to Inara, which also serves to distract her long enough for him to run back and hold off the approaching mooks.
- Earn Your Happy Ending: They even manage to earn some much needed cash. With how things usually end up, Mal is stunned by this turn of events.
- The Evils of Free Will: The Doctor and the Big Bad argue over this. Naturally, the Doctor wins.
- Foil: The Doctor and Mal, to each other. Both are damaged war heroes with a nasty case of Chronic Hero Syndrome and a natural charisma, but where Mal is gruff and slips easily into wrath, the Doctor is bouncy and slips more easily into Tranquil Fury.
- Genre Savvy: The Doctor, even more so than usual.
- Go Look At the Distraction: The Doctor throws a Hypno Trinket up in the air, hoping some brainwashed thugs will stare at it long enough for River to beat the snot out of them.
- Good Powers, Bad People: The Big Bad turns out to be an alien of a species known as empaths and healers.
- Great Offscreen War: Both the Time War and the war between the Alliance and the Browncoats are integral to the backstories and motivations of pretty-much every single character.
- Hannibal Lecture: The Big Bad does this to the Doctor. The Doctor later returns the favor.
- Hidden in Plain Sight: The Serenity crew tends to forget that a giant blue box from the Earth-That-Was is sitting around in storage. The Doctor himself also counts, as they are supposed to be looking for an alien, but they keep getting sidetracked.
- Hoist by His Own Petard: The Big Bad at one point successfully breaks into the Doctor's mind. It's exactly what the Doctor wanted him to do.
- Humans Are Bastards: The Doctor goes on one of his famous rants when he finds out what the Alliance did to River's brain.
- Hypno Trinket: These were used primarily to gain control over Reavers (as well as a few humans).
- I Did What I Had to Do: The primary reasoning of the Big Bad, as well as Zeke, the leader of a town plagued by Reavers.
- Idiot Ball: The Doctor even admits that his little It's Probably Nothing stunt was blindingly stupid.
- Implausible Deniability: Invoked when Inara and the Doctor are escaping from the enemy base).
The Doctor: You must be mistaken, Leftenant. The lady and I were just out for a stroll. You must have mistaken us for someone else.
- Irony: The Doctor is clearly enjoying himself immensely every time somebody mentions how stupid the idea of aliens is.
- It's Probably Nothing: While everyone is hunting Reavers in some woods, they all suddenly stop, thinking they heard something. The Doctor opts to barrel through anyway. Guess what he walks right into?
- The Lancer: Mal and the Doctor are essentially the heroes on their own shows. When stuck together, though, the Doctor acts as Mal's Lancer and vice-versa.
- Laughing Mad: Actually invoked by the Doctor. Everyone is duly freaked out by it.
- Living Ship: The TARDIS and River take a liking to each other.
- Masquerade: The enemy's base has the cover of a business. No one working there knows anything about their boss.
- Mind Control Device: See Hypno Trinket above.
- A Mind Is a Terrible Thing to Read: Subverted. The Doctor considers figuring out River this way, but besides the obvious problems, believes that it's so much more interesting to get to know people without it.
- Mind Over Manners: The only time the Doctor does anything with River's mind is when she explicitly allows him to.
- Mind Rape: The Big Bad pulls this on both Mal and the Doctor. The Doctor even uses that term.
- Mood Swinger: The author does an excellent job of capturing both David Tennant's expressions and the dizzying switches between maniacal cheerfulness, introspective angst, and Tranquil Fury that they accompany.
- Never Heard That One Before:
Big Bad: You cannot escape, Doctor!
- No, Mr. Bond, I Expect You to Dine: After Mal is captured by the Big Bad, some of his underlings try to convince him to join them over coffee. To their credit, it was really good coffee.
- No Name Given: The crew is less than amused that the Doctor refuses to tell them his name.
- Not That Kind of Doctor: When Jayne says they're going to use their doctor for treatment, the Doctor says he doesn't do surgery.
- Oh Crap: Mal thinks this when he realizes the enemy might be keeping him alive in order to torture him.
- One Steve Limit: River Tam, not River Song.
- Operation: Jealousy: Played with. Kaylee pretends to like the Doctor in order to make Simon jealous, but it's only to screw with his head. Well, that and she's quite happy to stare at his butt on general principles.
- Out-Gambitted: Well, of course. This is what the Doctor is for.
- Perpetual Poverty: The Serenity crew are in even more dire straits now; since the Miranda incident in the Big Damn Movie, they've got bounty hunters after them and people are even more reluctant to hire them.
- Pregnant Badass: Zoe's pregnant with Wash's baby at this point.
- Really Seven Hundred Years Old: Comes up when River mentions that the Doctor is too old for her. Mal, believing himself to be about the same age, feels rather put out by this.
- A bit meta, but Nathan Fillion and David Tennant are less than a month apart age-wise. Were the Doctor human and the both of them the same age as their actors, Reynolds would be right on the money.
- "The Reason You Suck" Speech: The Big Bad to the Doctor (see also Hannibal Lecture).
- Red Oni, Blue Oni: Mal and the Doctor.
- Relationship Upgrade: Mal and Inara are engaged by the end.
- The Sixth Ranger: By the end, the Doctor has more or less fulfilled this role.
- A Storm Is Coming: The last thing River says in chapter one, almost by trope name.
River: The storm. It's coming.
- The joke here being that in the new series the Doctor is kind of a bogeyman to lots of baddies, especially the Daleks, and one of the more frequently heard of the names they have for him is The Oncoming Storm.
- Strange Girl: Even a millenia-old alien is weirded out by River.
- Super Speed: Vharaj can dodge bullets.
- Tagalong Kid: When the crew hunts Reavers terrorizing a town, a kid comes along as a guide and manages to kill one. He ends up killed himself in a later attack offscreen.
- Talkative Loon: The Doctor comes off like this to the crew (mainly because there's no companion there to tell him to shut up), which often gets on their nerves. Eventually Mal concludes he's an escaped reader like River largely because of this.
- Techno Babble: From both sides.
- Tempting Fate: While infiltrating the enemy stronghold.
Inara: They seem to be expecting an auditor.
- Subverted, incidentally. Despite the Doctor's expectations, nothing of the sort happens.
- Utopia Justifies the Means: The Big Bad 's reasoning.
- Vagueness Is Coming: The way River often talks anyway. In this case, she predicts the Doctor at the end of the first chapter. By one of his scary names.
Mal: She said, and I quote, 'A Storm Is Coming.'
- Villainous Breakdown: Once the Doctor traps the Big Bad 's mind, he turns into jelly.
- Voice of the Resistance: Mal is recruited to be this. He turns them down.
- Weirdness Censor: A literal one. The Big Bad uses a device similar to what the TARDIS has to keep up the Masquerade at his hideout.
- Well-Intentioned Extremist: The Big Bad.
- What Year Is This?: When the Doctor begins to get an idea of where he is, he finally just gives up and asks this. It does nothing to help get people to stop thinking he's out of his mind.
- You Do NOT Want to Know:
Mal: Kaylee, find something for the doc to do. He don't need to be fussin' the whole time we're gone.
- You Shall Not Pass: During an escape, Mal does this so Inara and the Doctor can get out.