When the cease-fire between the human race and the shape-shifting Zygons is broken, war breaks out all over Earth. The Doctor must find the means to re-establish peace among the races before they completely annihilate each other.
SPOILERS AHEAD!
The Zygon Invasion acts as the follow-up to the Doctor Who 50th anniversary movie, The Day of the Doctor. We open with the two Osgoods, one human and the other Zygon, as they explain the terms of the Human/Zygon Peace Treaty, known as "Operation: Double". Apparently, 20 million Zygons have made their home amongst the human race in disguise with the intention of blending in and living in harmony. However, they explain that a breach of the treaty would require them to activate a device known as the Osgood Box, given to them by The Doctor in the event of this "nightmare scenario".
Once The Doctor realizes the Zygons are beginning an uprising, he has no choice but to return to UNIT and find out what they know. Director of UNIT, Kate Lethbridge-Stewart, shows The Doctor they've discovered the Zygon high command's secret base in an effort to have him unlock the technology found within and pinpoint their next move. After decrypting their files, he discovers a message containing footage of a Zygon splinter group murdering the old high commanders, taking their place, and calling for a revolution against the treaty, along with the repeating message of "Truth or Consequences". As it turns out, it isn't just a warning; Truth or Consequences is also a city in New Mexico. The Doctor decides to take a UNIT squadron to rescue Osgood, the only one capable of rebuilding peace, while Kate goes to Truth or Consequences to uncover its relevance.
Along with the strike team, The Doctor makes his way to the Zygon occupied village in Turmezistan where Osgood is being held captive. After a very intense standoff between the troops and a battalion of Zygons who have taken the form of their loved ones, the strike team ignores the orders of their commanding officer and is fooled into entering the building in question, where they are executed into piles of smoking ash. The attack prompts the field commander to call an airstrike on the area, leaving The Doctor only minutes to find Osgood and bring her to safety.
Meanwhile, in Truth or Consequences, New Mexico, Kate discovers the town is completely barren, save for a lone, terrified local sheriff. She proceeds to tell Kate the trouble started when one of the disguised Zygons revealed themselves accidentally, causing a panic and ultimately leaving everyone in town dead. Unwittingly trusting this sole survivor, the sheriff drops her rouse upon realizing Kate is alone, revealing herself as a Zygon. Taking Kate's form, it establishes complete control of UNIT, the only organization capable of halting their efforts, putting the final stages of their coup d'etat into place.
At long last, the ninth season of Doctor Who delivers an episode well worth a two part installment! The Zygon Invasion is definitely the best of the season so far. The supposed peace treaty established in The Day of the Doctor was never really touched upon again, so we never got to see if it all worked out. All we needed to know at the time was that London wasn't blown into a crater and peace between the two species was possible. Now that the walls are being broken down thanks to a faction of radicals, things are worse than ever, hence the phrase "nightmare scenario". Its been a while since The Doctor had to stop an actual world war from a hostile race outside of the usual invasion tactic, so this was a refreshing change of pace with a lot of dark turns and some pretty intense moments. The cliffhanger left us with Zygon Clara firing a rocket launcher at the plane The Doctor and Osgood are on, so we won't know if (let's face it, "how") they survive, but the momentum of this episode should make for some pretty eventful action in the next episode, The Zygon Inversion.