Mauritius 1681. The last dodos in the world are being killed by a combination of pigs and people. The last female is hiding in the undergrowth when she is suddenly plucked to safety by two humans in green overalls.
On the TARDIS the Doctor and Martha are deciding where she might want to go next. Unfortunately the limitless choice is inhibiting her so much that all she can come up with is a trip to the zoo. The Doctor is disappointed, not just by the mundanity of her choice but also because he finds the idea of cages offensive. When she realises that the bookmark he is using is a dodo feather she makes her mind up to see a dodo in its natural habitat.
The Doctor inserts the feather into a small hole in the console and the TARDIS follows its code to track down a dodo. While it is in flight he also gives her the I-Spyder book of Earth Creatures, telling her it has billions of entries. Each is awarded points, but nine billion are required to get a certificate.
The TARDIS eventually lands right next to a living dodo. Unfortunately, it is in a cage
The dodo appears to be in stasis in a Perspex box. As far as the eye could see there are more boxes of every size, each containing a different kind of animal. As soon as Martha and the Doctor step out of the TARDIS an alarm sounds and guards appear. They lead the time travellers down a long walk that passes boxes containing every imaginable kind of creature. Martha gradually realises that they are in a museum, in the Earth section (signs point the way to other planets such as Mars, Mondas and Tara.)
Eventually they are taken into a fairly ordinary office where they are introduced to a middle-aged woman called Eve. She wants to know what they were doing in the Museum of the Last Ones outside business hours. She explains that the museum covers an entire planet and contains the last remaining specimen of every creature that has become extinct in the universe. The museum staff can track each species until an alert tells them there is only one left, at which point they teleport down and retrieve it, putting it in stasis and leaving it on display in the museum.
Eve also tells them that exhibits are vanishing from the Earth section where the time travellers were found and as the most obvious culprits they are under arrest.
A young man, Tommy, bursts into the office, saying a Black Rhino has vanished. This is the fifth Earth specimen to disappear. When a guard confirms that the rhino was still present while the Doctor was in custody Eve is forced to accept his innocence. The Doctor follows a suggestion from Martha and produces his psychic paper telling Tommy they are agents from the Galactic Wildlife Trust. Eve, on the other hand, sees only blank paper but agrees to let them carry on with their investigations.
Tommy, the leader of the Earth specimen gathering team, takes them to the offices to meet the rest of his team. Martha is aware of a dizzy sensation and realises she is teleporting across the museum-planet to the Earth section. There are six Earthers: Tommy, Rix, Frank, Celia, Vanni and Nadya.
They are given a tour of the Earth section and Martha is astonished at the size and variety of the place, containing 300 billion exhibits in perspex boxes. The Doctor tells her they are only a few decades ahead of her own time. He is worried that they are all still alive, trapped in a permanent frozen moment.
He examines the box which had contained the rhino. He notices a keypad that controls the stasis field. When Tommy demonstrates how it works Martha notes the code he uses. Only the six Earthers and Eve have access to this code. The Doctor suddenly remembers that Eve's office has a display showing each species when there is only the last one left and thinks that if the rhino is still alive it should be on the display.
Back in Eve's office they find the rhino is on Earth. She gives the Doctor and Martha a pendant each that will teleport them and they travel with Tommy and Rix to a vast concrete warehouse. In the corner is a rhino, minus its horn. They locate a tiny office containing a chair, table and computer. Martha is aware that the warehouse has no external door and so the only way in or out is to teleport, suggesting the culpability of one of the Earthers.
On the computer the Doctor finds a list of missing creatures and their apparent price (in millions). Next to these are teleport coordinates. A book in the desk drawer contains a similar list but with different prices. They key in the coordinates for a quagga and teleport.
In her office Eve is looking at the display. The quagga's light has gone out but there is another light which should not be there. It belongs to a planet that had never known a single extinction and then vanished without trace. She cannot remember when it vanished: days, months or millions of years ago. But there is one survivor.
The time travellers arrive in the home of a rich woman. She is wearing the coat of a quagga. They try to find out who she bought it from but answers are unforthcoming so the Doctor contents himself by telling her that she is wearing the coat of one of twenty quaggas that are stuffed and exhibited on Earth and she has wasted 3.7 million pounds. As he transports away he tells Martha this is a lie he made up to infuriate this woman.
The next set of coordinates takes them to a caravan in a muddy field. Despite his denials they find themselves talking to Professor Douglas Dunnock, author of Fishy Fingers: Evolution from Sea to Land. He eventually confesses that he is keeping Mervin the missing link in his sink, and spent all the proceeds from his best-selling book to buy him, because Mervin disproves his scientific theories. Unfortunately he cannot tell them who he bought Mervin from.
Their next set of coordinates takes them to a sumptuous mansion in China. They find a young girl who bought the rhino horn to save someone, unsuccessfully. She is crying into a handkerchief patterned with dinosaurs, exactly like one they saw Tommy using.
They return to the warehouse and find Rix next to the skinned corpse of a quagga. The other Earthers arrive and Martha accuses Tommy of the crimes, citing the handkerchief as evidence. He explains they were Christmas presents from Eve, from the museum gift shop, and that they all have one. He produces his own from his pocket.
In a seemingly random move the Doctor switches his accusation to Frank who promptly produces a gun and confesses. Before he can use the gun he is charged down by the rhino. They all return to the museum. Martha goes with Vanni and Celia to the cafeteria while the Doctor and the others take Frank to Eve's office.
Frank is led off by security guards, the other Earthers are allowed to rest and Eve tells the Doctor he is the Last Time Lord and puts him in stasis in a perspex box. It is apparent that he is still conscious in the box and is reflecting on the Time Lords' attempts to keep him in one place when his natural habitat was to wander the Universe.
When Celia is sent down to Earth for another Last One she has no partner due to Frank's incarceration. Eve suggests that Martha goes with her, pretending that the Doctor agrees. They teleport to an oriental market and buy the last Chinese three-striped box turtle, or rather think they have. They find they have picked up the last one and have to return to the trader and then track down the old lady who is about to make the real last one into soup before reclaiming their prize. In this process Martha accidentally lets slip she is not a secret wildlife agent and is a trainee doctor. Celia takes her to the museum and says she is going to call Eve and get Martha to explain herself.
Once they have deposited the turtle a security guard arrives to take Martha but she clobbers him and makes a run for it. The museum is open now and full of visitors so she uses their cover to get back to the area where they left the TARDIS. And that is where she finds the sonic screwdriver. Nearby is a perspex box with a cover over it. Martha pulls the cover off and sees the Doctor. She types in the code on the keypad that Tommy used earlier but nothing happens so she puts the screwdriver and her teleport pendant into the keypad and presses every switch and button in every combination she can manage. This has the effect of freeing the Doctor. Unfortunately every one of the Earth exhibits has vanished simultaneously.
The Doctor takes them to the TARDIS and traces the animals, saying they have all returned to the exact place where they were collected from. Using the dodo feather he takes them back to Earth but instead of Mauritius they arrive next to the dodo in an alleyway in England. The Doctor speculates it is here because it was brought to England by a seventeenth century sailor. They are taking it back to the TARDIS when a scream draws them to a supermarket and they find a sabre-toothed tiger. This is puzzling because there is no conceivable way in which this creature could have crossed the Atlantic in its own time.
With the help of a fireman called Albert they rescue a pair of old ladies then lead the tiger onto the road where the Doctor uses his screwdriver to melt the surface of the road and trap the tiger's paws. Tommy arrives and is using his pendant to send the tiger to the museum but nothing happens except for the tiger sinking its huge teeth into his side. Martha attends to him, glad to see that the wound is not serious when they notice a second dodo. And another sabre-toothed tiger. In a shop window they see a bank of televisions showing news reports of tigers and dinosaurs running wild across the world. One of the dinosaurs promptly turns into the street and begins to bear down on them.
The Doctor uses Tommy's and Martha's pendants to send them (and the dodo) back to the museum. She uses her intercom on the pendant to call for help for Tommy, leaving him in the deserted Earth section, before creeping off.
The Doctor is saved from the Megalosaurus when it is attacked by a tiger, which it kills. He uses this diversion to get back to the supermarket where he finds Albert in his fire engine. Using the ladders he vaults over the dinosaur to get back to the TARDIS and uses the pendant he left there to freeze the creature. Then he uses the TARDIS computers to send the dinosaur back to the museum. Before returning to his adventure he asks Albert if he can drive the fire engine round the block with the siren on.
Martha makes her way to the cafeteria looking for the Earthers' quarters. A plain wall suddenly opens and out comes Frank on his way to the toilet. Martha suppresses her surprise that he is no longer locked up and pushes into the room which is a laboratory populated by dozens of dodo clones. She realises that Frank was selling clones of the animals in the museum, only using the originals when the clones were not sufficient for his purpose.
He tells her he is not from Earth but Kinjana where the people have the same body type. He is about to shoot her when Eve bursts in telling him she wants Martha alive. Martha is tied to a chair. Eve tells her that she was the one behind the cloning, using the money to pay for the museum.
The Doctor says goodbye to Albert and then investigates a dodo. He notices it is trying to bury an egg, then realises that the 'egg' is actually a bomb. Then he is attacked by another dinosaur. Back in the museum Frank is controlling the dinosaur but Eve stops him using it to kill the Doctor and zaps it back to the museum. The Doctor is aware from the television news that dodos all across the world are burying bombs. He returns to the TARDIS.
Eve tells Martha that Earth is the worst place in the Universe for extinctions. To evade the pressure of keeping up she plans to wipe out all life on the planet. If it all dies at the same time there can be no last ones of any species and she can forget about the planet completely. She will have Martha as a sole representative of the entire planet and that will be sufficient for her.
Eve leaves the room just before the TARDIS materialises. The Doctor bounds out of the door and snatches the gun from Frank's hand. He tampers with it and tosses it back. Frank runs off to fetch Eve and she returns after the Doctor has freed Martha but before they can locate a deactivating switch for the bombs. When Eve refuses to deactivate them herself the Doctor offers himself as an exhibit. Eve says she needs Martha too but she will still destroy the Earth. She speculates that she may have to destroy the Universe as well.
The doctor tells her that she is sadly misinformed about the nature of the Universe. She has only been collecting from the Milky Way and a bit of Andromeda. There are trillions of galaxies she hasn't even thought of. Eve is distraught, her mission is impossible to achieve. She raises the gun Frank left behind to shoot them but the Doctor's tampering with it earlier causes it to explode backwards. She is revealed to be an android. The Doctor unscrews one of her fingers and the bombs are all deactivated.
He heads off to Eve's office but cannot gain access to her central computer. The other Earthers are gathered there. Martha wonders if Frank has the password but realises he must have escaped. Rix says he would need to get his pendant back from Tommy. They race to the infirmary and find Frank by Tommy's bed. He takes all their pendants and is ready to escape when he produces one last egg bomb with which he plans to kill them all. Martha tries to get it from him but it falls on the floor. The dodo, which is fortunately still with them, sees it and follows her instinct to bury it, unseen by Frank, in his bag full of money. He teleports away to the warehouse on Earth seconds before it explodes.
The Doctor says he needed Eve's password to return all the missing animals. Tommy says it is "Hr'oln", the name of Eve's first pet.
The Doctor uses her computer and the TARDIS to send all the animals back to their own time, plus a few years before their extinction. In fact he picked them up from the moment Martha freed them all so that none went to Earth at that time, except the Megalosaurus which gave him the idea in the first place. He goes on to send every animal from every planet back to its home.
Before they leave the Doctor and Martha find a secret room containing the suspended form of Hr'oln, last of the Cirranins. The Doctor frees her to let her tell her story.
A scientist and explorer, she returned to her own planet expecting a hero's welcome only to find it destroyed by a catastrophic war. Flying on she found a planet inhabited by a humanoid species. Because her own appearance was so alien she constructed an android in their image so that she could deal with them: Eve. She gave her all her own knowledge and together they devised a teleportation system to let them visit other planets. When the people of this new world were wiped out by plague Hr'oln was distraught. She told Eve that they must stop any other species from dying out. Eve did not understand and so Hr'oln told her that when she died her species would be gone, too.
Eve's misunderstanding was compounded. She instantly put Hr'oln into stasis and the next thing she knew was when the Doctor unfroze her 500 million years later. Eve had thought she wanted the last one of every species collecting to stop it from dying out, not every species being saved by science and medical techniques.
The newly revived Hr'oln decides to rebuild Eve and use her cloning skills to recreate a new life, perhaps her own species.
They return their dodo to the cloned flock in the laboratory. The real last dodo finds itself back among its own kind in the seventeenth century. Martha finds that the 8963400 points she gets for a Time Lord and the 2 points she gets for a human give her 9000001, enough for an I-Spyder certificate.