This is a timeline of events that occurred during the 2000s.
- Casey went to fish with her father and John, Casey's uncle. Casey's Father would teach her how to shot. After Casey would see John, pretending to be an animal and convinced her to come “play” with him and proceeds to molest her. After this she threatened to shot John but ended up not doing it. Her father would later die from a heart attack.
- Elijah at a bar talking with an worker of the train station.
- Elijah sabotaging the train.
- Philadelphia's Train Crash: After a job interview in New York City, David is returning back from to Philadelphia, David had been caught in a train wreck that has killed 131 passengers.
- David woke up in a hospital, and was told by Dr. Dubin that not only is he the sole survivor, but he hasn't broken one bone or has had a scratch on him.
- David later attends a mourning service for the other 131 passengers. After the service Dunn finds a card on the windshield of his car with the words "Limited Edition" engraved on the front. David flips the card which has black marker writing which says "How many days have you been sick?".
- David would return to work as a security guard, David would ask his boss Noel if he every been sick.
- Later that night David would go home, and talked to Audrey about if he ever been sick, neither of them are able to recall him ever being sick though.
- David would take Joseph to the Limited Edition comic book art museum, where he meets the man responsible for the card: Elijah Price. Price would tell David about his disease known as Osteogenesis Imperfecta type 1, which means his bones are very frail and easily breakable. Prince would theories that if there was someone like him in the world then there would be someone that is the opposite of him. He goes on to explain he has seen the city's disasters, ranging from a plane crash, and a hotel fire. Price was looking for key words to find what he was looking for. When he heard about the train crash and heard the words "Sole survivor" he believes that he has found the man he was looking for. This interests David at first until Price mentions that he believes Dunn to be a modern day superhero, someone that comics based themselves on. This throws Dunn off and he accuses Price of being a scam artist. He then leaves with Joseph to go home.
- At home, Audrey tells David that she believes it is a miracle that he survived that train and wishes they could start over again, even going as far as asking him out on a date.
- The next day at work, Dunn gets a call that someone is trying to get in the stadium on a bogus ticket. He goes to see the person who reveals himself to be Elijah, who finds it strange that a person that doesn't think he is a superhero, takes a job that requires him to protect people. While walking past a queue of people waiting to be allowed into the stadium, David reveals an instinctive power to sense criminal behaviour or past wrongdoings by touch, intuiting that one of the men in line is carrying a gun. Though Elijah considers this further proof of superhuman powers, David is once again dismissive.
- However, Elijah decides to follow the man out of the stadium, but trips while descending a flight of stairs and shatters several bones - though he is vindicated when he discovers that his quarry is indeed armed.
- David returns home from work to workout with Joseph helping him with the weights. It is there, where they discovered David has limitless strength.
- Next few weeks, Elijah now wheelchair bound is assigned to physiotherapy and, as luck would have it, his therapist is David's wife, Audrey. Over the course of their time together, he learns that David supposedly injured himself in a car accident, ending his football career; however, Elijah believes that David faked his injuries and abandoned his future in sports in favor of his marriage to Audrey a theory eventually proved true.
- Dunn later tries to test Price's theory, when he gets a vision that one of the customers is selling drugs. After searching the man finding nothing, he begins to doubt himself. Dunn then gets a call from Joseph's school, that he got hurt in a fight defending a girl.
- While in the office the principal remembers Dunn from back when she was a school nurse. She reminds him of the time he almost died in the swimming pool, which answers Elijah's sick question.
- Back at home Audrey tells David that Elijah has been stalking her telling her his theory. Before he can react, Joseph enters the room with his gun intending to shoot David to prove he is a superhero. David manages to convince him not to, by threatening to leave and go to New York.
- Dunn confronts Elijah over this and tells him he has been sick from drowning. Before leaving David warns him to stay away from his family.
- After a David and Audrey date he gets a message from Price stating that every hero has a weakness, and David's is water. David later goes to the train yard to see the remains of his train in the accident.
- David later goes to the train yard to see the remains of his train in the accident. He looks and sees a big hole where his window seat used to be.
- Dunn later calls Elijah asking for advice. Price tells him to go to where people are and that the rest is up to him.
- David goes to the subway station where he reaches out making sure everyone touches him. He sees visions of a woman in red stealing, a man in yellow assaulting an interracial couple, a date rapist, and a man in orange invading a family's house.
- Rescue of the Kidnapped Family: Dunn follows the man to the house using his rain poncho as a disguise. While sneaking in he notices the man of the house dead, and two children tied up. Dunn unties the kids and goes to the master bedroom where he sees the mother tied to a radiator. He looks around the room for The Orange Man, who sneaks up behind him and knocks him out of the window. David lands in a pool where he nearly drowns, but the kids save his life. Dunn later goes back and kills The Orange Man by strangling him to death. When he unties the mother, she was already dead. Dunn then goes home and rests not feeling sad anymore.
- The following morning, he secretly shows a newspaper article on the anonymous heroic act, featuring a sketch of David in his hooded rain poncho, to his son, who recognises the hero as his father.
- David attends an exhibition at Elijah's comic book art gallery and meets Elijah's mother, who explains the difference between villains who fight heroes with physical strength versus those who use their intelligence. Elijah brings David to the back room of his studio, extends his hand, and asks David to shake it. Upon doing so, David sees visions of Elijah orchestrating several terrorist disasters, including David's recent train accident, causing hundreds of deaths. David is horrified, but Elijah insists the deaths were justified as a means to find him. Calling himself "Mr. Glass", a nickname his peers had used to taunt him with when he was growing up, he explains that his own purpose in life is to be the villain to David's hero.
- David reported Elijah's actions to the police, and that Elijah was convicted of murder and terrorism and committed to an institution for the criminally insane.
- Kevin was abused by his abusive, obsessive-compulsive mother.
- Graham discover's that his wife Colleen Hess was involved in a car accent, Colleen's last words come back to Graham was "swing away".
- Graham discovers a crop circle in his field. While investigating the crop circle with the local law enforcement, Graham learns of animals becoming violent across town. Morgan is forced to kill one of the family dogs when it turns violent against Bo. They hear reports of crop circles appearing around the globe, and there are reports of lights from invisible objects over Mexico. Later, Graham and Merrill find the farm is being watched by a tall dark figure which disappears into the fields when they give chase.
- They hear strange noises over a baby monitor, but cannot find their source. Graham approaches the crop circle but on seeing a green leg sticking out of the cornrows, flees back to the house. After opening up to Merrill about the death of his wife, noting that her last words were "tell Merrill to swing away", Graham goes to visit Ray, the first time since the incident.
- When Graham is gone, Merrill and the children watch a news report about footage taken of an alien creature in Brazil, showing that the aliens can blend into their surroundings. Merrill joins the children in wearing tin foil hats, believing the aliens can read their minds.
- At Ray's, Graham finds Ray is bleeding from an injury but otherwise apologetic for the accident. After Graham accepts his apology, Ray departs for a nearby lake, saying "they" do not like water. Graham finds Ray has trapped one of the aliens in his pantry, and tries to see what the alien looks like using a kitchen knife under the door; the alien grabs at him, and Graham reacts by cutting off its fingers before fleeing. On his return, and hearing news that more lights have been seen in the skies across the globe, the Hess family decides to stay at their house instead of leaving for the lake, barricading the doors and windows.
- After an emotionally charged dinner, they hear the same noises on the baby monitor before their television signal drops out, and place the final barricades and defences before they gather together. As the aliens attempt to gain entry into the house, the family discovers they have left the attic door unguarded and quickly retreat to the basement. The aliens assault the basement door and in the subsequent chaos the light goes out as Graham and Merrill prevent their entry. However, Morgan suffers an asthma attack when the aliens attempt to enter by way of an old coal chute.
- By morning, reports on the radio reveal that the aliens have left Earth as suddenly as they arrived. Graham leaves the basement to locate Morgan's asthma inhaler, the others following him. But they discover an alien, the one trapped in Ray's home, is still there, and takes Morgan hostage.
- Graham told Merrill "swing away" with a baseball bat from his minor league days. Merrill attacks the alien but not before it attempts to poison Morgan by spraying him with a toxin from its body.
- Graham recovers his son when the alien drops him and takes Morgan outside with his medication. Merrill continues to attack the alien, causing it to fall onto the ground, knocking over one of the glasses of water Bo had left and splashing it with water. The water reacts like acid on its skin, making it scream in agony. Merrill strikes the alien against furniture where it is doused with water full on its face, and dies.
- Outside, Graham administers Morgan's medicine and waits for his son to wake up, hoping that due to his lungs being closed from his previous asthma attack he was spared. Then, Morgan wakes up and the family rejoices.
- Some time later, the Hess family has recovered from the incident and they appear to be doing much better than before. In the final scene, Graham is shown returning to his priestly duties, apparently having regained his faith.
- Casey had managed to escape from John, yet, her body was filled with scars so she could be able to inform the police about what she passed, leading to the uncle's arrestment.
- In New York City's Central Park, people begin committing mass suicide. Initially believed to be caused by a bio-terrorist attack using an airborne neurotoxin, the behaviour quickly spreads across the northeastern United States. Elliot Moore, a high school science teacher in Philadelphia, hears about the attacks and decides to go to Harrisburg by train with his wife, Alma. They are accompanied by his friend Julian and Julian's eight-year-old daughter Jess.
- Julian's wife is stuck in Philadelphia but is expected to meet them in Harrisburg. The train loses all radio contact en route and stops at a small town. They receive word that Philadelphia has been attacked by the toxin and Julian's wife was not able to get on the train to Harrisburg, instead taking a bus to Princeton. Julian decides to go look for her, leaving his daughter with the Moores while he hitches a ride. However, when they get to Princeton, it has already been hit by the toxin. Succumbing to it, the driver runs the car into a tree and Julian sharpens a piece of glass.
- Elliot, Alma, and Jess hitch a ride with a nurseryman and his wife. The nurseryman believes that plants are responsible, as they can release chemicals to defend themselves from threats. The group are joined by other survivors and split into two groups, with Elliot, Alma, and Jess in the smaller group.
- When the larger group is affected by the toxin, Elliot realizes that the plants are targeting only large groups of people. He splits their group into smaller pockets and they walk along, arriving at a model home. Two other groups arrive on the property, triggering a neurotoxin attack, signaled by what appears to be wind blowing through the vegetation. The next house they come upon is sealed, its residents trying to protect themselves from the toxin. Elliot's attempts to reason with them are deemed unsuccessful when the residents shoot Josh and Jared, two teenage boys whom Elliot had earlier befriended.
- Elliot, Alma, and Jess next come upon the isolated house of Mrs. Jones, a negative, elderly eccentric who has no outside contact with society and is unaware of the current disaster.
- The following morning, Mrs. Jones becomes infected with the toxin. Realising that the plants are now targeting individuals, Elliot locks himself in the basement but is separated from Alma and Jess, who are in the home's springhouse out back. They are able to communicate through an old talking tube, and Elliot warns them of the threat. He expresses his love for her before deciding that if he is to die, he would prefer to spend his remaining time with her. The three leave the safety of their buildings and embrace in the yard, surprised to find themselves unaffected by the neurotoxin. The outbreak has abated as quickly as it began.
- Three months later, Elliot and Alma have adjusted to their new life with Jess as their adopted daughter. On television, an expert, comparing the event to a red tide, warns that the epidemic may have only been a warning. He states that humans have become a threat to the planet and that is why the plants have responded aggressively. Alma discovers she is pregnant and embraces Elliot with the news.
- In the Tuileries Gardens at the Louvre Palace in Paris, France, a scream is heard and everyone freezes in place as the wind rustles through the trees, signifying another attack by the plants.