One morning in every city and town in the world, the human race wakes up to face the most surprising invasion yet. Everywhere, in every land, a forest has grown overnight and taken back the Earth. It doesn’t take the Doctor long to discover that the final days of humanity have arrived.
Clara Oswald and Danny Pink are chaperoning a number of Coal Hill students on an overnight stay at London’s Natural History Museum. They wake up to find that London, as well as the rest of the globe, has suddenly been covered by forests in a matter of hours. The Doctor learns of this when one of Clara’s students, Maebh, finds his TARDIS parked in the forest-covered Trafalgar Square and witnesses the change. The Doctor calls Clara to confirm their situation, causing Danny to react resentfully upon finding out Clara still secretly keeps in contact with him. Clara and Danny lead the group to Trafalgar Square to reunite with the Doctor. As they talk about the trees, the Doctor suspects that the only way the trees could have grown was due to some external influence. They all board the TARDIS and, as the Doctor works with the controls, Danny finds Maebh’s notebooks, which Clara had accidentally left aboard whilst on her last trip in the TARDIS. The notebooks are filled with pictures of an angry sun striking down trees. Clara explains that Maebh’s sister Annabel disappeared a year prior leaving Maebh traumatised, and she has been on special medication that quiets voices in her head. The Doctor realises that Maebh is central to the appearance of the forest, the condition allowing her to tune to some other communication frequency. When they see Maebh is not with the rest of the children, the Doctor and Clara race out to find her.
They find Maebh has dropped personal items along the path to allow her to be followed. They encounter a government service team trying to burn a path through the forest but the trees are able to control the oxygen nearby to prevent them from being burnt. As they continue along, the Doctor explains to Clara that Maebh’s drawings show a giant solar flare, similar to the one that destroyed the Bank of Karabraxos (“Time Heist”), that he confirms is occurring presently and is due to strike the Earth that day. The Doctor is curious as to why Maebh knows this.
As they continue after her, they hear sounds of wild animals, which the Doctor believes are from the London Zoo, its cages torn asunder by the trees’ growth. They rescue Maebh from several wolves chasing her, realising too late that the wolves themselves were being chased by a tiger. Danny arrives with the rest of the students to help scare off the tiger. As they regroup, Maebh runs off, waving her hands wildly, which the other students say is a tic that she has had since her sister disappeared. Catching up to her, Maebh explains that she thinks she created the forest from a dream she had after her sister’s disappearance. The Doctor is able to interpret her ranting and motions, and adjusts the local gravity near her with his sonic screwdriver, revealing a number of glowing bug-like creatures that circle Maebh. They speak through Maebh, explaining they have persisted throughout time, and were called to Maebh. They cryptically describe how they created the forest as they had done before in the north and the south. When the beings express pain while under the field of higher gravity, the Doctor lets them go. The Doctor mulls over this information and determines that the Earth is truly doomed by the solar flare. Clara suggests they save the group of children with the TARDIS. However, when they get to the TARDIS, Clara insists the Doctor leave on his own, refusing to abandon Danny and unwilling to be the last human left alive, and that for all the times the Doctor has saved the Earth, it is time for Earth to allow the Doctor to escape.
The Doctor regretfully takes off in the TARDIS and monitors the solar flare, but inspiration hits him and he quickly returns to Earth and catches up with Clara and the others. He has interpreted the cryptic message from the beings, and determined that they were responsible for protecting the Earth from disaster during the Tunguska Event and the Curuçá impact by rapidly growing trees across the planet to buffer the effects of these impacts that should have otherwise extinguished all life on earth. The sudden appearance of the forest now is to prevent damage to the planet from the flare. However, Danny reveals that they saw news that the government plans to use defoliating agents to strip the leaves from the trees to allow them to be burnt, which would affect their ability to stop the flare. The Doctor uses the TARDIS to hack into the world’s cellular network, and Maebh reads off a message prepared by her and the rest of the children warning earth’s population not to harm the trees; she also asks for her sister Annabel to return. The Doctor offers the group the opportunity to witness the solar flare’s impact from the TARDIS, but Danny says he’ll take the children back home; Clara joins him for part of the way during which Danny reveals he has figured out that Clara lied to him about traveling with the Doctor, but is willing to accept her apology and continue their relationship. The Doctor and Clara watch the flare harmlessly strike the Earth; this is also watched by Missy on her tablet, calling the result a “surprise”. Later, in Clara’s flat, the Doctor and Clara watch as the new trees disperse, and the Doctor explains that humanity will forget about this, just as they did after the previous events, but their lingering memory would become part of mankind’s fairy tales.
Maebh, having reunited with her mother, who had been searching for her, returns home during this. As one of the new bushes disperses, they find Annabel waiting for them there, and the family has a tearful reunion.