Don (Robert Carlyle) and his wife Alice (Catherine McCormack) prepare dinner for their group of survivors in a heavily reinforced cottage somewhere in rural, infected Britain during the Original Outbreak of the Rage Virus. As they eat their meal, they suddenly hear a young boy banging on the door begging to be let in. Don reluctantly opens the door to let the child inside, who says he is from Sandford and has been fleeing from his parents, who are now infected. Moments later, a large horde of Infected discover the hideout and break in, quickly overwhelming the group. Alice refuses to leave without the boy, and a panicked Don abandons Alice and escapes in a boat, emerging as the sole survivor.
After the outbreak, over the course of twenty-eight weeks, the Infected have all seemingly died, primarily of starvation, and Britain is declared relatively safe again. An American-led NATO force enters the country and begins repopulating London with both old and new residents. Chief medical officer Major Scarlet Levy (Rose Byrne) is startled by the sudden arrival of children. Among the children are Tammy (Imogen Poots) and Andy (Mackintosh Muggleton), Don and Alice's children who were in Spain during the initial outbreak. During their subsequent medical inspection, Scarlet notes Andy's heterochromia, a trait he inherited from his mother. Andy and Tammy are subsequently admitted to District 1, a heavily-reinforced, fully functional section of London on the Isle of Dogs guarded by the United States Army, including Sergeant Doyle (Jeremy Renner) and helicopter pilot Flynn (Harold Perrineau).
They are reunited with their father Don, who is now head caretaker of District 1. Inside their new penthouse, Don tearfully recounts his escape, saying that Alice was killed by the Infected. But he misrepresents the truth, saying that he witnessed Alice's death, to hide the fact that he fled and abandonded her to her fate. The next day, the two children slip out of the safe zone to return to their old home, where Andy discovers Alice, dishevelled but alive. Andy, Alice and Tammy are found by the US Army and taken back to District 1, where Alice is decontaminated while Tammy and Andy are detained. A blood test reveals that she is infected with the Rage Virus, but not displaying any symptoms, labeling her an asymptomatic carrier, as evidenced by her bloodshot eye. Though Scarlet wants to keep Alice alive to seek a possible vaccine or cure, she is overruled by her superior, Brigadier General Stone (Idris Elba), who wants Alice killed to prevent another outbreak of the virus.
Don visits his children in a holding room, where they confront him about his version of Alice's death. He then visits Alice in her isolation cell, and asks for forgiveness, which she seemingly does, but then they kiss; the Rage in Alice's saliva infects Don, much to Alice's horror. Now infected, he brutally kills Alice and goes on the prowl in District 1, attacking and infecting or killing anyone he comes across. The outbreak forces the area into lockdown, but not in time to prevent Don from forcing his way into one of the safe rooms, where he begins to infect the crowds of confined civilians. Scarlet rescues Tammy and Andy from containment, and they flee together as chaos spreads to the streets. Doyle and the soldiers are first ordered to shoot only the Infected, but the chaos escalates into "Code Red": a general extermination of the populace. Doyle, unable to bring himself to comply with the order, abandons his post and escapes with Scarlet, the children and another survivor (Raymond Waring) as District 1 is firebombed and destroyed. Meanwhile, large numbers of the Infected, including Don, escape the bombardment, occupying the ruined city.
Stopping to rendezvous with Flynn's helicopter at the derelict remains of Regent's Park, Scarlet informs Doyle that the children, who may have the same immunity to the Rage Virus as their mother, could be the key to curing the Infection. Flynn arrives by helicopter to pick up Doyle, but refuses to take anyone else - citing that they will be blown out of the air if he attempts to break the Code Red protocol. Suddenly, as a massive horde of Infected approach the park, the other survivor grabs on to the helicopter skids, screaming at Flynn to take him with him. The helicopter is sent into a spin from the extra weight, however, Flynn regains control and sweeps over the approaching Infected, killing them with the rotor blades, and dislodging the man. He then tells Doyle to head to Wembley Stadium, and Doyle heads off with Tammy, Andy and Scarlet.
The group breaks into an abandoned car to escape the Infected and the clouds of poisonous gas being vented into the city by the military. In the process of starting the car by pushing it, Doyle is killed by soldiers with NBC suits and flamethrowers. Scarlet drives into the London Underground to evade a pursuing helicopter, where she and the children continue on foot, guiding their way with the night vision scope on Doyle's rifle. When they are separated, Scarlet is ambushed and killed by Don, who has followed them. Shortly after, Don comes across Andy and attacks and bites him. Tammy arrives and shoots Don to save Andy, who remains symptom-free like his mother (apart from his eye, which turns bloodshot). The children continue to Wembley Stadium and are picked up by a reluctant Flynn, who flies them out of Britain and across the English Channel.
Twenty-eight days later, someone calls for help in French over the radio of Flynn’s helicopter, which turns out to be abandoned somewhere in France. A group of Infected are then shown running out of a subway exit towards the Eiffel Tower, revealing that the Rage Virus has spread to mainland Europe.
The DVD release of 28 Weeks Later has two deleted scenes from the film on the special features.
A scene in the canteen of District One, where Andy goes and sits down beside Scarlet. Don and Tammy arrive and they all formally introduce themselves to Scarlet. Scarlet tries to explain that the Rage Virus is possibly still alive, but concedes that it is probably gone. Though the full scene was cut from the film, some shots from it can be seen in the finished film.
After Tammy kills Don, and Andy runs away from her, down into the subway, he sits down on a station platform and waits for the Rage Virus to take him over. A train suddenly arrives, and Andy gets aboard. He sees Alice, his mother, in another carriage, and runs towards her. The two meet and embrace, but Andy then realises that it is just a hallucination, and that he is still in the Underground subway with Tammy.
In March 2007, Danny Boyle announced plans to create a third film in the 28 Days Later series, which will be given the title 28 Months Later with a 2013 release date. Boyle has stated that his thoughts are to set the movie in Russia. In June 2007, it was announced that if DVD sales of 28 Weeks Later did well, Fox Atomic would consider producing the third film.
In July 2007, while promoting Sunshine, Boyle revealed that he has a story formulating for the next film. "There is an idea for the next one, something which would move [the story] on. I've got to think about it, whether it's right or not." Boyle also revealed that he would return as the director. Alex Garland (the screenwriter of the first film), on the other hand, said in October 2010: "When we made 28 Days Later, the rights were frozen between a group of people who are no longer talking to each other. And so, the film is never going to happen unless those people start talking to each other again. There is no script as far as I'm aware."
- Originally, when Danny Boyle, Alex Garland and Andrew Macdonald first considered producing a second film in the series, they considered calling it 29 Days Later. Several ideas for a 29 Days Later film were put forward, before it was decided to use the 28 Weeks Later idea:
- Jim, Hannah and Selena from the first film would probably return.
- The story of an SAS team sent into infected London during the time frame of 28 Days Later to rescue the Queen or the Prime Minister.
- A story which focuses on the impact the initial outbreak of Rage has had on society.
- 28 Weeks Later was originally going to end with Flynn's helicopter parked in France twenty-eight days after Tammy, Andy and Flynn leave Britain. However, Juan Carlos Fresnadillo and Enrique López Lavigne conceived the ending in which the Rage Virus spreads to France as a last-minute idea before the film was to be handed over to Fox Searchlight for distribution.
- Though in the finished film, the scenes in which Doyle, Tammy, Scarlet, Andy and Sam try to escape District One take place at night, in the trailer for the film, they are in broad daylight. This is because the scenes were filmed in daylight, and a new computer technique was used to darken the image and make it appear in the finished film that it was night.
- When Don is running from the cottage to the dock, fresh tire tracks can be seen in the ground.
- The DLR train carrying new citizens from the airport has "Greenwich" on the front. Greenwich is across the river from the Isle of Dogs, so it wouldn't have been part of District One.
- Scarlet is shown to wear her hair in a ponytail while in uniform. In real life, women in the US Army are not allowed to wear their hair beneath the collar.
- Flynn's helicopter changes multiple times. He falls asleep in an Aerospatiale Gazelle. When he attempts to rescue Doyle, he is flying an Aerospatiale A-Star. When he lands in the stadium to rescue Doyle and the children, he is once again flying an Aerospatiale Gazelle.
- When Tammy and Andy leave District One to re-visit their old home, they are shown crossing Tower Bridge, which, as they have started their journey from the Isle of Dogs, means they are travelling south across the Thames, but the next shot shows them passing the London Gherkin, which is built on the North Bank.
- When Scarlet kills the infected Weise, blood splatters over the window, covering the area of the detainment room's window where his hands are. But in the shot where Weise's body collapses to the floor, most of the blood on the glass has gone.
- While trying to escape with the survivors, Scarlet is shot on the inside-front of her left leg, which she bandages up. Later in the abandoned Regent's Park, when she re-bandages her wound, it has moved to the outside-front of the leg.
- Wembley Stadium and the London Gherkin are both shown fully built in the film. However, 28 Weeks Later apparently takes place between 2002 and 2003; the Gherkin wasn't fully built until 2004, and construction for Wembley Stadium did not even begin until 2003.
- The uniforms the US Army wear are ACU's (Army Combat Uniforms). The US Army did not start using these until 2007-2008; as 28 Weeks Later is set in 2002 - 2003, they should be wearing BDU's (Battle Dress Uniforms).
- When Doyle, Tammy, Scarlet and Andy are fleeing Regent's Park, Doyle fires his gun three times to kill four Infected. However, at the third shot, two of them fall, but since they weren't lined, it would be impossible to kill both men with only one shot.
- When the survivors are driving to escape the toxic gas, the windshield is covered in blood, which disappears in the next shot, then reappears.
- The infected Don beats Scarlet to death with the butt end of Doyle's M4 rifle. However, through the scope, it appears that he is using the other end to beat her to death.
- After Andy is bitten and infected by Don, he becomes a Carrier of the Rage Virus like his mother, and thus his left eye's sclera partially turns red. However, in the scene where Tammy and Andy confront Flynn at Wembley Stadium, Andy's left eye is clearly visible, and his sclera is all white again.