Bill is on her date with Penny and as they walk, Bill tells Penny about the Doctor, and the fact that their fake date was broken up by the Pope. It seems that Bill is never going to have a private life because it ends when soldiers burst in followed by the Secretary General of the United Nations. It seems that he's looking for the Doctor and felt that Bill would know where to find him. Are companions on some kind of watch list? How is it that leaders of the earth always seem to know who the Doctor is hanging out with at any given time? Bill of course denies knowing the president because she thinks the Secretary General is talking about Trump, only to be informed that in times of crises, the Doctor is the president of the world. This of course is when Penny decides that maybe it's time to just call an Uber. Poor poor Penny.
The Doctor is in the Tardis when Bill knocks on the door complaining that he's been in there for hours. Even when Bill tells the Doctor that the Secretary General wants to see him, the Doctor says no. Clearly the UN must know exactly who they are dealing with because the Tardis is already on a plane headed for Turmezistan, where a pyramid has just appeared. The pyramid is right in the middle of a hot zone because the Russian, Chinese, and American military have formed a sort of stand off in the area and war is looming. Once they land, the Doctor announces that the pyramid is a show of strength and decides that earth's military should simply target it and destroy it. This is clearly the Doctor acting out of fear because his first action is never violence - he doesn't even really to turn to violence as a last resort. The Doctor outsmarts people and beats them at their own game. Of course, the attack is unsuccessful and as Nardole points out, violence is never the answer.
One of the complaints I had about Extremis, is the fact that we don't know what the red robbed aliens really want? In the Pyramid at the End of the World, we learn that the aliens want to make the earth theirs. To accomplish this they have studied earth and have chosen this particular moment in time to make their move. The aliens have determined that the earth is going to end and to prove their point, they show the leaders of the American, Chinese and Russian military, along with the Secretary General of the UN and the Doctor what the earth will look like in a year without their intervention. The robed aliens offer to intervene but only if they are asked to do so by someone who has power and it must come from a place of love. Even though the Doctor begs him, the Secretary General of the UN decides to surrender but his surrender is not deemed legitimate because it is coming from a place of fear. The Secretary General quickly turns to dust. Damn, these aliens are not messing around.
To ensure everyone knows just how much shit the earth and humans are in, the aliens set the doomsday clock to three minutes to midnight. This means that whatever is going to bring about the end of the world is already underway. The leaders of the army decide that they aren't going to follow orders and refuse to fight each other but this does nothing to reduce the threat. It's enough for the Doctor to realise that the pyramid and threat of a war are actually nothing more than a distraction to what the real issue is.
It turns out that the real problem is at Agrofuels Research Operations. It all hinges on Douglas, who's so damn hungover that he doesn't do his job correctly, thus creating a lethal pathogen which ends up killing him. That's one hell of an advertisement against drinking and showing up to work hungover. It's Erica, his fellow coworker who realises that something terrible has happened and takes actions to ensure that her other co-workers are safe and attempts to limit the damage. Unfortunately, the lab is due to vent the air into the atmosphere shortly and when this happens the jig is up so to speak. Erica is shocked when the Doctor arrives but given what is going on, she rolls with the punches.
Back in Turmezistan, the military leaders decide that they are going to surrender because it's the best thing for the earth, even though they don't know what the cost of surrender is. Everyone makes their way back to the pyramid where the three leaders offer their surrender, only to be told that their surrender is not pure because it does not come from a place of love but pragmatism and strategy. Damn these aliens are hard to please. Now the decision of whether to surrender the planet or not belongs to Bill because she speaks for the Doctor.
At the lab the Doctor sends Nardole back to the Tardis because he only gave Nardole discount lungs, but warns him to keep the Tardis close by. Nardole isn't on the Tardis two minutes before he passes out. The Doctor gets down to work and quickly realises that the best way to deal with this situation it to set off an explosion to destroy the threat. As the Doctor works, the Doomsday clock starts to move away from midnight and the aliens start messing with their probability machine. The Doctor tells Bill to get out of the pyramid.
Bill and the Doctor really haven't been travelling together for very long but when the Doctor reveals that he's still blind and cannot work the combination lock because he cannot see it, Bill feels compelled to return to the center of the pyramid. The Doctor tells Bill not to consent and not to ask for help and that she has to let him die. Bill decides that she won't let the Doctor die and decides to ask for help and that his sight be returned. Bill is tested and unlike the others who went before her, Bill passes and the deal is struck.
The Doctor's eyesight is returned to him and works the combination lock in time to get to safety. The Doctor is then told by the aliens that he can now see their new world.
Even blind the Doctor is absolutely a force to be reckoned with. He was not defeated by the aliens or the bacteria, he was defeated by a piece low tech that the sonic screwdriver could not fix. Despite the end result this was no victory for the aliens, no matter how heartbreaking Bill's decision was. Yes, she chose to save the Doctor but she also did so with the belief that the Doctor would also save them from whatever bind they put themselves in.
Okay, the Doctor's blindness has been resolved and this will put him into a better position to deal with the robe aliens, who by the way still don't have a name. What I am most interested in is what this all means for the Doctor, given this:
This to me looks like a regeneartion (yes, I'm tearing up) but there are five more episodes still to go, not including the Christmas episode. In an interview, Capaldi did say that he's already filmed his regeneration scene. Damn it Moffat, you've left enough for me to spend the next week trying to figure out what the hell you're playing at.