The Doctor was making some repairs to the TARDIS console and had sent Amy and Rory to Liao Dynasty China for Chinese food. Unfortunately, they mistoke the palace for a restaurant, offended the Emperor and had the guards on their tails. The Doctor is in the middle of TARDIS maintenance when a spear is hurled into the Doctor's record player and the TARDIS takes off.
The TARDIS bumped into another space ship, forcing the latter to crash on Earth. The collision also created a portal to another planet inside the TARDIS. The Doctor explained the portal as a dimensional lesion. He asked Rory to hand him the sonic screwdriver to examine the lesion properly. However, Rory tossed it and the sonic ended up on the other side of the lesion. On the Doctor's orders, Rory walked through the lesion onto the other planet to find the screwdriver before returning to the TARDIS.
While Rory was getting the Screwdriver, the Doctor sent Amy to get a Kardanian Vortex Tuner and a Zardak holofield trap from his drawing room and put them together for him. Using the newly-invented dimensional equaliser, the Doctor closed the lesion. The TARDIS picked up a distress beacon from the ship they ran into. They go to investigate.
The group arrived underground in London in 1605, three hundred years after the crash. They discovered that the proximity of the two alien ships was creating more lesions thoughout London. If they did'nt close them soon, all of London will be sucked into the lesions to another planet. While the Doctor hunted down and closes lesions, he sent Amy and Rory to find the ship. They spotted two suspicious figures talking about a plan to kill the king.
They followed them to their headquarters in the sewers. Using the chopsticks from their takeout, Amy picked the lock into the secret tunnel and they spy on the men. They were part of the Gunpowder Plot to assassinate the King of England. Rory noted a detail that wasn't in the history books: a female conspirator named Lady Winters.
Amy created a distraction by taking advantage of a plotter's fear of rats, using her takeout to lure a bunch of them to him. She noticed Lady Winter's eyes glow green. Rory steals a document listing the plotters' final meeting before the plot comes to fruition. With the information in hand, Amy tells Rory to find the Doctor while she follows Lady Winters to see if she's not from Earth. Amy loses her in an alley, where a green goo is all that's left of her. A black cat with green eyes passes her.
Elsewhere, the Doctor is trying to close a lesion and instead diverts the location on the other side to where Amy is. He sees a green-eyed cat turn into a Rutan, prompting him to jump through to save Amy. Amy's scream reveals the Rutan's sensitivity to high-pitched sound. Taking this into account, the Doctor uses his screwdriver to scare the Rutan off. The Doctor concludes the ship they bumped into is a Rutan ship.
Amy is also led to the conclusion that Lady Winters is the Rutan they just fought off. She explains to the Doctor that she is working with the Plotters. The Doctor encounters another lesion. This time a man is in shock from having found it. The Doctor closes the lesion, bringing the man out of shock. The man tells the Doctor about a orphan named Charlie who has had encounters with Lady Winters, the "green lady", and more lesions. The Doctor has the man take him to the other lesions while he orders Amy to look for Charlie.
Amy finds Barnaby, a friend of Charlie's, but he refuses to talk to her for fear that she'll give him the plague. Amy finds an apothecary who offers to make her a posie said to ward off the plague in exchange for its ingredients. Using the posie, Amy gets Barnaby to talk to her. Barnaby hasn't seen Charlie in days. He's been too busy looking after his younger sister, Annie, to look for him. The last time anyone saw Charlie, he was wet and had been underground.
Meanwhile the Doctor and the man, called Mr. Plum, have tracked down two more lesions, which he seals. Amy arrives shortly after the second one is sealed and explains what she knows about Charlie. Based on those clues, he's been hanging around the drains and near them is where the Rutan ship is.
Meanwhile, Rory has been exploring the London underground and finds Sontarans coming out of the water. Before he can make his escape, he is caught by their mind-controlled servant, Black Rod. The leader of the group, Major Kaarsh, wrongly deduces that Rory is working for the Rutans and is tricked into revealing the Sontarans and Rutans are after the Rutan ship because it contains something of strategic value.
Kaarsh decides to imprison Rory as part of a plan to bargain with the Rutans, leaving Black Rod to guard him. Rory sneaks up on Black Rod, steals the mind control device and gets away. Black Rod explains he is in the service of the king and investigates threats to his person. He was investigating the Gunpowder plot when he came under the control of the Sontarans. After he guides Rory out and away from Sontaran patrols, he tells Rory to find his friends while he returns to his post.
Amy and the Doctor find Rory. All three are aware of the Sontarans in the sewers. Rory gives the Doctor the paper detailing the plotters' next meeting, only to discover it is blank. Using the fireplace in his drawing room, the Doctor reveals the details of the meeting have been written in invisible ink. By heating the paper, the Doctor learns that the next meeting is to take place at the Duck and Drake at precisely 9:00.
Using his Psychic Paper, the Doctor tricks the plotters into thinking he works for King Phillip and earns their trust by doing tasks vital to the Gunpowder plot. While the Doctor talks to the plotters, Rory and Amy find a trail of Rutan goo and plan to follow it to the Rutan Ship.
On their way, Rory and Amy discover the Sontarans' weak spot on the back of their neck. Rory and Amy enter the Rutan ship via a lesion and deactivate its security system. They soon run into the brain of the ship, revealed to be alive. The ship doesn't appear to be interested in Rory because he has Rutan goo on him. Amy, on the other hand, is nearly killed by the ship, Rory saves her by giving her some of the Rutan goo. With the ship no longer trying to kill them, they enter the control room, where they find Charlie, captured by the Rutans.
They free Charlie. He thinks they are working with the Rutans and runs away, stealing a green sphere from the Rutan console. However Charlie has left behind his sling shot and a bag of marbles, which prove effective against Sontarans. Armed with the slingshot, Rory and Amy fight their way through the sewers and get back to the surface. While Amy and Rory are dispatching Sontarans, the Doctor and the conspirators meet with Lady Winters.
To the Doctor's surprise, the conspirators are planning to use forty-one kegs of powder instead of the historical thirty-six. After the meeting, the Doctor convinces Winters that he intends to help her get off earth, citing the problems her ship and she are causing. Winters claims she needs three things: a pair of energy conversion rods, Parliament removed from the top of the ship and the momentum from the explosion.
The Doctor sends Rory and Amy to look for the rods. They learn that the rods were integrated into a clock and a globe. Rory and Amy collect the rods and bring them back to the ship and install them. Meanwhile the Doctor and Lady Winters encounter a stray Sontaran, whom Winters kills. Winters explains that her ship was carrying a pair of doomsday bombs to wipe out the Sontaran species.
Winters leaves for her ship. At the same time, Guy Fawkes, the brains and most famous of the plotters, gets the Doctor's help with the plot. After complications caused by the Rutan ship, Guy and the Doctor get to the kegs. The Doctor convinces Guy to use five fewer kegs and light the fuse ahead of schedule.
With this, the Doctor uses the TARDIS to transport Parliment into orbit, safely away from the explosion and the Rutans. Lady Winters calls the Doctor and accuses him of stealing the weapon, demanding it back or else. Amy realises that Charlie has the weapon. He is hiding in Parliament and is under attack by Sontarans. Rory also realises that the ceremonial mace has the other weapon incorporated into it.
The Doctor gives Amy and Rory a Rutan stun device that needs to be repaired. The group splits up. Rory and Amy will go after Charlie and the Doctor will go to Black Rod and get the staff. Unfortunately the Rutans and the Sontarans have turned Parliament into a war zone. The Doctor finds Black Rod and uses Psychic Paper to convince him that he is one of Lord Salisbury's agents. Unfortunately they wind up cornered by a Sontaran.In the meantime, Amy has found Charlie and Rory has repaired the stun device with a musket. After clearing away a few Rutans, Rory finds the weapon Charlie stole. Amy distracts the Sontarans by getting them into a fire fight with a Rutan patrol. Rory frees Charlie. Unfortunately the Sontarans win the fight and come back. Rory barely saves them with his last marble.
Elsewhere, the Doctor signals Black Rod to distract the Sontaran, while he gives him a much needed whack to the back of his head with the mace. The Doctor removes the weapon on the end of the staff and reconfigures the weapon so it is non-functional; if he had made a mistake, that corner of the universe would have been destroyed.
Unfortunately they run into a patrol personally led by Kaarsh. The Doctor lures a patrol of Rutans led by Lady Winters into the Sontaran patrol. The Doctor gives each group a weapon, one reconfigured to wipe out the Rutans but not telling them which is which. This forces both sides into a stalemate and makes them leave. Kaarsh takes this news in stride; the Doctor's intervention has made their war with the Rutans "honourable" again. Lady Winters, on the other hand, is furious; the device would have ended the war.
With the Rutans and Sontarans gone, the Doctor returns Parliament to its proper place on Earth and goes to greet Guy. The Doctor assures him that even though he failed now, people will still remember him. He boards the TARDIS and leaves history to take its course as Guy continues with the plot, just in time for King James' guards to come in and arrest him.