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Time is running out for the Doctor as Downing Street announces mankind's first Interplanetary War.

Rose is taken home, but a spaceship crashes in the Thames and London is closed off... Enter the Slitheen!

Charles Dickens and the Doctor team up as corpses stalk the streets of Victorian Cardiff.

The Doctor takes Rose on her first voyage through time: to the year five billion, when the Sun is about to expand and swallow the Earth. She is cautious and soon starts to question her reasons for joining The Doctor. But amongst the powerful alien races gathering to watch on Platform One, a murderer is at work. Who is controlling the mysterious and deadly metal spiders?

Rose Tyler meets a mysterious stranger called the Doctor, and realises Earth is in danger.

Suzuha explains how SERN was able to build a time machine and use it to rule the world in 2036. She explains she plans to travel to 1975 to acquire an IBN-5100, but soon discovers her time machine has broken down as a result of the storm on the night Rintarō stopped her from leaving. Rintarō leaps two days before the completion of the time leap machine in order to get Hashida to help fix Suzuha's time machine, whilst Mayuri suggests they also help find Suzuha's father, using his badge as a clue. Suzuha gives Rintarō her Divergence Meter, which keeps track of the magnitude of differences between timelines, and tells him about how he founded the resistance against SERN in the future. After spending the day searching for Suzuha's father, Suzuha gives her thanks to Rintarō before he receives a lead on Suzuha's father from a badge maker.

Rintarō makes several time leaps, but no matter what, Mayuri always ends up dying in some way. In one of those leaps, Rintarō calls out Moeka and holds her at gunpoint, making her reveal that SERN have targeted the lab due to the creation of the time machine and their plan to publicly announce it. As Rintarō falls further into despair, Kurisu gets him to reveal what he knows and offers to help him try to save Mayuri. She sends Rintarō to just before she completed the time leap machine, where he tells her past self what he knows. As they discuss what the cause of Mayuri's death could be, they are greeted by Suzuha, who tells them that in order to save Mayuri, they need to find a specific World Line. She takes them to the crashed satellite, which turns out to be her time machine, and reveals she is "John Titor" and has come from the year 2036.

Right after Moeka kills Mayuri, Suzuha rushes in the lab and creates a distraction, allowing Kurisu to use the time leap machine to send Rintarō back in time to 5 p.m. of the same day. Rintarō drives everyone away from the lab, but wastes most of his time searching for Mayuri. By the time they try to escape the area, the bomb threat has stopped the subway and Mayuri is killed when Moeka runs her over with a car. Rintarō manages to escape the clutches of SERN and leaps to the past again. Using his knowledge of Mayuri's movements from his previous leap, he manages to find her sooner and they visit a different subway station. However, Mayuri dies again when Mr Braun's daughter, Nae, accidentally pushes her in the way of an oncoming train. Devastated, Rintarō vows to keep leaping to the past until he manages to save Mayuri.

With the ability to utilise the LHC, Kurisu completes her 'time leap machine'. However, Rintarō, still tortured by the texts he has received, decides against performing an experiment, instead suggesting they announce it to the public. As the lab members decide to have a party, Kurisu comes into conflict with Suzuha, who claims she is destined to become a SERN spy, but Mayuri manages to calm things down. As a bomb threat is televised, Suzuha, after hearing about the lab's connection to SERN, suspects something is terribly wrong and leaves. Just then, the lab is attacked by a group of armed men, led by Moeka who reveals herself to be from SERN. Demanding Rintarō, Kurisu and Hashida hand over the time machine and come with her, she decides Mayuri isn't needed and kills her.

Rintarō discovers that a television in the electronics shop below the lab is the key to the time slot in which D-Mails can be sent. Kurisu then theorises that it might be possible to send memories back in time in the same manner as D-Mails, effectively allowing people to 'leap' to the past. As Rintarō goes into town with Mayuri to look for parts Kurisu needs, running into Moeka along the way, Suzuha tells Rintarō that Kurisu works for SERN, though Kurisu denies this when asked. Kurisu tells Rintarō about the troubles she has with her father, who grew to hate her when she surpassed him in scientific prowess, though cheers up when Rintarō offers to help them reunite. As Mayuri and Kurisu decide to have a sleepover at the lab, Rintarō receives another sinister text message warning him that he knows too much, later learning that the lab is connected to the SERN network without the lab members' knowing.