The Transformed (comic story)

 was the second story in Doctor Who: The Ninth Doctor.

Summary
The Doctor, Rose, and Captain Jack, bouncing back from their most recent adventure with a destructive doppelgänger, run into a most unexpected face! As the Doctor struggles to keep Rose apart from an element of her future she cannot know, Jack discovers another twist on his missing past that complicates his present!

Part one
When Mickey Smith met the Ninth Doctor, he hated him. The Doctor stole his life and everything that mattered to him. But then, the Doctor changed. And it proved impossible to hate the Tenth Doctor. Someone who gave Mickey a new life, one better in every way. And now, Mickey finds himself in desperate need of the Doctor, frantically trying to call him.

Or more accurately, frantically trying to rid himself of the Ninth Doctor who irritably demands to know how Mickey got his number. Mickey scoffs and invites the Doctor to leave bitterly saying that he wanted "the other one." Realizing that Mickey is from his future, but also that he's in trouble, the Doctor follows him, despite Mickey's protests, both the personal ones and the worry to any damage the Web of Time could suffer should Rose and Jack see Mickey. Before the argument can continue, a scream draws their attention. Running off, the two find a gargoyle confronting two people, Mickey pulling out a gun and shooting down the woman, allowing the gargoyle to fly away. Enraged, the woman tackles at Mickey at superhuman speeds, breaking his gun, before she and her companion fly off after the gargoyle. Helping Mickey up, the Doctor demands an explanation.

Back at the TARDIS, Rose and Jack ponder where the Doctor has run off to before Jack reads off the date and time, sending Rose running outside. Following, both Jack and Rose note that they're usually aren't auroras in San Francisco. In the skies, the two superhumans attack the gargoyle, sending it crashing into a trolley that slides towards Rose and Jack. Swooping down, Dean stops the runaway car with his bare hands, earning the admiration of Rose and the locals before he flies off to join Georgie.

Elsewhere, Mickey recaps the situation to the Doctor. When the strange lights began to appear in the sky, people initially thought nothing of it until residents of the city began to exhibit superhuman abilities. And then the gargoyles began showing up just as people began to go missing. UNIT's response was, of course, to issue a D-notice. With Mickey tied up in the Czech Republic, Martha Jones investigated alone, suspecting Krillitanes. As the Doctor makes a joke about Mickey being married, the man snaps at him to stop. Because, as a gargoyle helps illustrate by carrying the Doctor away, the sonic screwdriver gets their attention.

Atop the Golden Gate Bridge, Dean and Georgie meet with Chris and Henry to discuss Dean's heroics and their missing friend, Brandon. As arguments are sent back and forth, Chris points out the gargoyle carrying the Doctor. Far from being concerned, the Doctor is amazed by the creature, even finding human DNA beneath its scales before the superhumans arrive.

Elsewhere, Rose drags Jack atop an apartment complex, ostensibly for the view, but Jack suspects that she just wants a shot at seeing Dean again. As Rose jumps on the ledge and jokes about having a flying man catch a falling woman, she trips and falls to the ground only for her to start levitating a few inches from death. Dean then appears and offers, over Jack's protests, to show Rose how to use her powers.

Meanwhile, the other superhumans fight the gargoyle causing it to lose its grip on the Doctor. As he plummets, another gargoyle, one with distinctly feminine feature catches him. Drawn by Mickey, the gargoyle lands the two in parking garage with Mickey snapping at an overeager Doctor that the gargoyle is Martha and his wife asking the Time Lord to refrain from his smart-arse comments for once. Struck dumb by how little Mickey thinks of him, the Doctor asks what happened. Continuing his story, Mickey reveals that Martha's powers developed by the time that he'd arrived in San Francisco but that that was the first stage of mutation from human to gargoyle.

Part two
As the Doctor scans her, Martha levels Mickey a glare for getting the wrong Doctor. Irritably, the Doctor demands to know what the Doctor has found. Using his sonic as a light, the Doctor reveals that the aurora borealis is nothing of the sort. They're an afterimage of an artificial wormhole that's running through Earth, like a railway line through a hill, but the wormhole has been created using punchway technology. Normally this wouldn't be an issue but given San Francisco's history, energy from the wormhole is leaking out and mutating people. Fortunately, assuming they're complete, the mutations can be reversed. Pushing Mickey out of sight, the Doctor meets with Jack who reveals that Rose is starting to mutate. Sending him after her, the Doctor and Mickey race back to the TARDIS only to be barred by Martha, who insists on coming along.

Materializing at Trading Post Shirov-three, the Doctor guides Mickey and Martha to the Celestial Hyperloop Corporation, owners of the punchway, which is being operated by Glom. Annoyed to see the Doctor again, Glom calls for security who quickly down the trio.

Back in San Francisco, Rose is introduced to the other superhumans only to find them harassing a frightened gargoyle. When she tries to stand up for it, a fight breaks out between her and Georgie which Dean breaks up only to find he is mutating into the final phase. As the other realise that Brandon is the gargoyle, Dean flies away in shame with Rose following. When Jack catches up, he reveals what's causing the mutation and how it can be reversed. Though he tries to disrupt the wormhole's energy, Jack only succeeds in opening up a portal to Shirov-three which, again, over his protests, Rose leads the others through.

At the Trading Post, the security webs have worn off and Mickey quickly downs the guard before an alarm sounds about the hyperloop's collapse. A frantic Glom calls up the bus' camera to learn that Rose is the cause. Grabbing both the Doctor and Mickey, Martha flies into the wormhole.

As the superhumans gape at the oncoming traffic, their mutations begin to accelerate, prompting them to try and seek shelter in the bus only for security to bar them access. Crashing in through the back, the Doctor and Mickey take control, collapsing the portal and sending the bus crashing on San Francisco bay.

As everyone picks themselves out of the wreckage, the Doctor calls Glom for pickup before a headcount reveals that Dean has vanished. Speculating that he was thrown out of time, Jack promises to scan for him when they're back in the Time Vortex. As cooler heads start to prevail, Rose confesses to the Doctor that she thought she saw Mickey for a minute. As Mickey and a restored Martha reunite, the Doctor laughs off such a notion.

In the 1970s (or possibly the 1980s) two UNIT agents are attacked by the fully mutated Dean calling it in back to headquarters and their commander, Harry Sullivan!

Characters

 * Ninth Doctor
 * Rose Tyler
 * Jack Harkness
 * Mickey Smith
 * Weevil
 * Martha Jones
 * Georgie
 * Deano
 * Gargoyles
 * Chris
 * Henry
 * Glom
 * Harry Sullivan

Continuity

 * This story takes place immediately after COMIC: Doctormania.
 * Mickey recalls how the Doctor "changed", (TV: The Christmas Invasion) and how their relationship was made all the better because of it. (TV: School Reunion, The Age of Steel, Doomsday, Journey's End)
 * This story sees Mickey briefly play companion to the Ninth Doctor. Since this story is set after the events of The End of Time, this is the first time in the Doctor's timeline where he takes Mickey on as a companion, whilst for Mickey, it's his latest trip with the Doctor (but his first with the Ninth). Thus, Mickey technically takes this Doctor up on his offer to travel with him. (TV: World War Three) Similarly, Martha, while in her transformed state, takes a trip in the Ninth Doctor's TARDIS, making it the first time in the Doctor's life where she does so, but the latest trip for her.
 * The Doctor, in his next incarnation, will find himself in another situation where he encounters someone at the wrong point in their timeline, due to receiving a message meant for his future self. (TV: Silence in the Library / Forest of the Dead)
 * The Bad Wolf meme can be seen on the sideway of a spacebus. (TV: The Unquiet Dead et al.)
 * The Doctor says that San Francisco has a "history", which influenced the wormhole to give nearby humans powers and mutations. (TV: Doctor Who, PROSE: Unnatural History, AUDIO: The Gift)