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Luna knew something was off from the moment she had first met this Doctor.
No, not the Doctor. This imposter. He was acting like the Doctor, he was using the Doctor's TARDIS, but everything about him felt. Off. She wasn't sure what felt off about him, but something did. He was nice enough to her, and he saved the day the same way he always did. He spoke of the Doctor's past as if he knew her friend - pointed out the street on Totter's Lane, referenced Susan by name - but that was still not enough.
Any imposter, any shapeshifter, any liar would know that information. It just had to be wrenched out of the real Doctor. Where ever they were.
She got her answer after destroying Conrad's Wish World. After defeating Omega and the Ranis. After the imposter version of the Doctor fell off a balcony, returned to UNIT and 'saved the day' like he had always done. Then, he left. To 'save Poppy'.
Save. He was even behaving like the Doctor. At some point the ruse had to break! At some point, he had to reveal himself. This was such a fucked up little game of his. She knew he was lying, he had to be lying.
And that was when she saw the Doctor again. The real Doctor, her Doctor. He looked older, hair thinning and eyes narrow, but it was still him. He reached out and held her, and she told him everything. The imposter that stood in her best friends place, who had been pretending to be the Doctor for gods knew how long. She had no idea when he'd been replaced, or even how. She just knew he had been replaced.
"How do you think he got this information?" He asked, pressing buttons on the memory TARDIS console - the imposter had the real one so this one had to suffice for now.
"I don't know," Luna said, "I'm thinking… Infostamp, biodata, some sort of memory transfer…"
In response to biodata, his eyes widened.
"Yes, yes, that's it!" The Doctor exclaimed, "Luna, I believe the man you've been travelling with is the real form of Omega,"
"Not the giant mutant dragon?"
"Oh, heavens no," he continued, "do you remember what happened - Amsterdam, my biodata was used by Omega to gain a new body,"
"But it was falling apart…" Luna trailed off.
"Ah yes, but remember we recieved that distress signal from Jolly Chronolodays?" The Doctor explained, "Omega, who believed he was me…"
That was all Luna needed to hear. The man she'd been travelling with was Omega, who believed he was the Doctor. For 11 whole faces, 11 whole lives, 11 silly, lying 'Doctors' who weren't even the Doctor.
"We have to stop him!" Luna exclaimed, "we need to find Poppy, who knows what he's gonna do to her!"
"Let's go to UNIT and warn them of the deception," the Doctor said, "they might have his last location,"
Luna grinned. They were going to stop Omega! She and the real Doctor were going to save the day from that imposter!
What she failed to notice was the smirk on the Doctor's face - an expression that should've looked odd, but in Luna's delusion addled mind it didn't.
Omega had indeed replaced the Doctor. Just not in the way Luna had expected…