Sam Horowitz excitedly reveals his great discovery to the assembled media (and a party of schoolchildren) in the Great Hall of the New York Natural History Museum. It is a perfectly preserved mammoth. Unfortunately, the mammoth is not dead. It revives and begins to rampage through the hall.

Elsewhere in New York the Doctor is eagerly introducing Amy to the Universe's perfect burger when they see a brief filmed clip of the mayhem. Racing down to the museum the Doctor blags his way through the police cordon with a combination of psychic paper and a special UNIT code. Commander Strebbins is less than impressed to have her authority usurped but lets the couple enter the now-deserted museum. The Doctor hears the mammoth coming through the walls and scales a column, helping Amy up beside him: not to escape but to leap onto the Mammoth's back. They notice a kind of intelligence in the creature, almost as if it is reading the notices on the walls before they climb aboard. It charges around, trying to unseat them. Even Sam gets involved in the action, removing his jacket and playing the matador, but the creature runs past him down a corridor to the exit. The Doctor has realised that the mammoth's skeleton is metal but its flesh is real. It charges into the street and is brought down by a volley of tranquiliser darts. One also brings the Doctor down.

Strebbins notices that Amy has been talking to a young officer, Oscar Henderson. She pulls Oscar to one side and tells him that the Doctor used a UNIT code. She doesn't want UNIT usurping her authority and orders Oscar to keep tabs on Amy and the Doctor.

Sam Horowitz finds refuge in the basement of the museum where he is found by his friend, Polly, who had brought her elementary school class to the unveiling. She asks him where he found the mammoth. He recalls the day he was cataloguing reindeer droppings and found a scrap of paper claiming to reveal the location of dinosaur bones near Svalbard. He followed the trail and came home, instead, with the mammoth.

Oscar arrives at the Midtown Police Station to discover that Amy has sent the entire police force outside with coffee and doughnuts while she sits with the unconscious Doctor. When the Time Lord wakes up she tells him he has been out cold for six hours and the mammoth is in the zoo. They sneak out the back of the station and borrow a squad car. Oscar arrives in time to see them leave.

As the sun sets over New York they steal into the zoo and locate the mammoth pacing in its cage. With a burst on his sonic screwdriver the Doctor disables the mammoth. Almost at once its belly drops to the floor, revealing a brightly lit interior, something like an alien space ship. A green ball of energy spreads out from the mammoth and expands across the city. An army of tiny soldiers assembles on the deck inside the mammoth. The Doctor tells Amy that this is an invasion. They are troll-like creatures, heavily armed, each about seven centimeters tall. Their general, Erik, tells the Doctor that he is leader of the 99th Vykoid Expeditionary force and he demands that the humans surrender. He adds that his army will take no lives, only slaves to work in the Desiccated mines of Cassetia 2. The Doctor tells Amy that these mines are in asteroids made entirely of Space-Boar dung. He refuses to surrender so the general instigates the Temporal Lock. Another wave of energy passes over them. At once its effects are clear: the Vykoids are suddenly moving much more quickly than the human eye can see.

Fully equipped in seconds, the army prepares to move out. Throwing herself at them to stop them, Amy finds herself lying down, tied up, almost instantaneously. The army moves away and Amy realises that the Doctor has been taken with them. She raises her hand and sees that she is no longer restrained. She follows the trail of the soldiers to the road outside the zoo where it vanishes so she heads back to the squad car only to find Oscar parked nearby. Summoning her most authoritative voice she demands she supply a tracker dog. He does so, against his better nature.

Meanwhile, Strebbins has researched Amy and found that she is a kissogram girl from England with no connection to UNIT. She instigates the Night Storm strategy that gives her total control of the city but since the entire communication network is down she has to send a runner with the message.

No sooner has the tracker Alsatian been delivered than the lights of New York go out. As they head towards the centre of town bricks begin to fly at them. Windows smash, lampposts are dragged down and debris is hurled about as if by invisible hands. Amy surmises that this is to clear the people off the streets. She tells Oscar that the mammoth contained tiny alien invaders and urges Oscar to look at them through his binoculars. They see a squad of riot police confront the aliens who, at super-speed, disarm the officers and replace their weapons with comedy items like umbrellas and traffic cones. When Oscar steps in to face the Vykoids he is not only disarmed but undressed and then redressed in skirt and lacy gloves with a tiara. Amy picks up his discarded gun but knows that the Doctor wouldn't want her to use it. Thinking of him, she remembers that she has his psychic paper in her pocket. She looks at it and sees a message from the Doctor saying that he is below her. She kisses Oscar goodbye and races to a Subway station.

She makes her way down the tracks until she comes to another station where dozens of people have been tied up on the platform. All, apart from the Doctor, are unconscious. He tells her that the Vykoids use sedative drops in the humans' eyes but he cried his out. They flee down the track only to find that the Vykoids are sending a train towards them. They dodge into an alcove and climb a ladder to the surface. Elsewhere, Strebbins learns that her entire force has been removed from the streets and sets out with a dozen cadets to retake the city.

The Doctor and Amy return to the museum and find Sam and Polly in the basement. After determining that Sam isn't an alien and part of the plan, the Doctor tells Polly that she has what he needs to fight the Vykoids: children. He says that the aliens are rounding up the strongest New Yorkers and designating them for slave work but the children of the city are invisible to them. He rounds up Polly's class and takes them to her apartment. Then he divides them into pairs and sends them to the highest points in the city to spy on the Vykoids. After this he takes Sam to the zoo to look at the mammoth. Amy persuades Sam to get into the mammoth while they close it up just to see what happens. When they let Sam out a few seconds later he complains that they left him inside for ages, telling them that the mammoth interior is immune to the Time Freeze.

Strebbins and her men arrive in front of City Hall and are promptly caught in a giant net. The Commander is taken down to the Vykoid scientist's lair where a Vykoid, Lars, is put onto her head and hidden by a cap. He assumes control of her mind. The same is done to hundreds of NYPD officers.

Another pulse of green energy restores the power to the city and New York springs back to life as the night ends. Looking at a television in a shop window, the Doctor and Amy see Trinity Wells interviewing Strebbins. They wonder why Trinity is wearing a ridiculous hat. The Doctor realises that the Vykoids have taken over the police just as a line of NYPD officers behind him take off their hats to reveal the grinning Vykoids on their heads. They leap into a taxi and the Doctor races across town, shaking off four pursuing police cars. They arrive at the zoo to find Oscar and some of the children. The children leap out of Oscar's car to say they found a massive glowing ball at the top of the Statue of Liberty.

The Doctor, Amy and Sam get into the mammoth and drive it across New York. They notice that the Vykoids, no faster than them now, are keeping the people of the city on the streets and herding them to Broadway to avoid a supposed terrorist threat. Oscar makes his way to where Strebbins is and pulls his gun but realises he has not got the will to shoot either her or her Vykoid controller.

The mammoth 'swims' to Liberty Island and then crashes through the ticket barriers, before mounting the steps inside the statue. General Erik watches their approach with disbelief. He can't see what the Doctor is hoping to achieve. As the mammoth bursts into the Vykoid control room it is disabled by thousands of tiny darts. The Doctor pulls himself out with his companions close behind and grabs the general's baton which he recognises as a control device. He uses it to slow the Vykoid/police but stops playing with it when he sees that the general has Amy at gunpoint. Amy and the Doctor are tied up and dumped in the torch of the statue where the Doctor takes a look at Sam, now with a Vykoid controlling him. The Doctor tells Sam to fight against the control while the Vykoid uses him to pull levers and flick switches on a control panel. With an effort, Sam wrenches the Vykoid from his hair and hands him to the Doctor. The Doctor scans the tiny warrior with his screwdriver then touches the sonic to the peak of the torch. Satisfied he steps down.

Thus, when the Vykoids use their teleport to send the first batch of New Yorkers into slavery it is his soldiers that vanish from the heads of the police. The Doctor enters and tells the General that Earth has a great champion: Amy Pond. The Vykoids retreat into their mammoth and depart.