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As Doctor Who continues its season of miracles, the episodes just keep getting better and better. “The Zygon Invasion” proved that last night, as it took the subjects of modern warfare and terrorism and surprisingly explored them in an in-depth manner for a family friendly show. Yet with the surprisingly dark tone of this week's episode, there's one question that stand out as Bonnie – Clara's new Zygon double – is about to shoot down The Doctor's plane, taunting him that his companion and all of U.N.I.T. are dead. That question is, is she telling the truth?
For background, let's go back to when Bonnie, who we still assumed was Clara, leads the U.N.I.T. forces in London to the underground chamber of the Zygons. We learn that there are tons of “pods” there, holding the humans that they have taken the forms of for some reason or another. Once Jac, Clara's companion, for lack of a better term, realizes that the pods aren't Zygon doubles and that Bonnie's order to fire is an act of sabotage, the jig is up and everyone in the room is murdered. This moment is where the question of Clara's existence starts to come into focus.
So the first possibility, which is the most likely, is that Clara isn't dead. While the Zygons don't need to keep the human they're impersonating alive in order to keep their image, we did learn from Osgood that they do need them for more in-depth details – such as memories. Seeing as Bonnie's been palling around with The Doctor since Clara investigated a local disappearance, she would need Clara's memories to suitably fool everyone who knew her. Most importantly, she would need those memories to fool The Doctor, as he would be the first person to notice something was up.
Of course, the other possibility could give us a hint towards how Clara is written off the show. Again, Zygons do not require the original host to maintain their appearance. Seeing as The Doctor spent most of “The Zygon Invasion” away from the erson he thought was Clara, he might not have been around her long enough to realize something was up. So if Bonnie really did kill Clara, along with all of U.N.I.T., odds are The Doctor will somehow take her on as his companion. Now whether it's because he's been fooled / he allows Bonnie to come into his confidence is still up for grabs. But the most likely scenario in this unlikely situation is that The Doctor takes Bonnie as a reminder of Clara / a token of his dedication to peace with the Zygons. Which means that Bonnie would either turn on The Doctor and eventually be dispatched, or would be attacked by someone who learns she's a Zygon.
The fact that we're even asking questions like this after watching “The Zygon Invasion” is proof that the Doctor Who writing staff has found a way to make the show work again. I felt Season 8 was mostly a wash, especially when it came to the squandering of Clara's character, but Season 9 is doing interesting things with her and the rest of the show, again. If you came into Season 9 expecting to cheer on Clara's departure, you hopefully have already reversed that attitude by this time.
We can see what answers next week brings when “The Zygon Inversion” airs on BBC America on Saturdays at 9 p.m. ET.