Outside the grounds of his high school, Light Yagami discovers a notebook that claims to be able to kill anyone whose name and face is known to its owner. He initially dismisses the so-called "Death Note" as a hoax, but, after testing its powers, he discovers that these claims are indeed real. The original owner, a shinigami named Ryuk, approaches Light and explains that the notebook now belongs to him. Since Light is the new owner, he is the only one who can see and interact with Ryuk. The shinigami also says that when Light's time to die comes, Ryuk will be the one to write down his name in his book. Light decides to use the Death Note's power to rid the world of evil and become the god of a new, peaceful world.

As criminals begin dying from inexplicable heart attacks left and right, Interpol convenes to discuss the phenomenon. Unable to come up with an explanation for it, they turn to the world's top-ranked detective, L, whose true identity is a well-kept secret. L speaks to the Interpol representatives through a computer and an electronic voice, promising them that they are dealing with mass-murder and that he will soon confront the killer whom the general public has been calling Kira (a play on the Japanese pronunciation of the English word killer). This displeases Light, who has been going to great lengths to keep the Death Note hidden, since learning that Ryuk becomes visible to anyone who touches the book. L tricks Light into revealing that Kira lives in Japan's Kanto region with a fake television broadcast. Having played right into L's hands, an enraged and humiliated Light swears to eliminate L.

Police authorities discuss the "Kira case" with L. Upon inquiring about the time of death of the victims, L concludes that Kira is likely a student with a naive concept of justice. He requests data on how the victims were publicized and begins to suspect that Kira has access to police information. Because the police officer in charge of the Kira case, Soichiro Yagami, is Light's father, Light can monitor the authorities' movements. Meanwhile, Ryuk tells Light that he is being followed. He also explains that not only do shinigami get the lifespans of people they have taken before their time, their eyes can see everyone's name and lifespan floating above their heads. He gives Light the option to trade half his remaining lifespan for the eyes of a shinigami, just like Ryuk's.

Light tells Ryuk that he is trying to create an ideal world where no criminals are left unpunished and that as the god of such a world he cannot sacrifice half of his life for the shinigami eyes. Light begins experimenting to find out how much control he has over how a criminal dies. He tries to have prisoners escape or draw L's face before they die. When they fail to do so, he learns that the Death Note is not all-powerful. Using this knowledge, Light devises a plan to find out who has been following him. Light has a drug dealer touch the Death Note and makes him hijack a bus before he dies. During the hijacking, Light gets his tracker to reveal that he is Raye Penber, a Federal Agent from the United States employed by L and his associate Watari.

One week later, Light follows Penber onto a train and forces him to write down the names of his fellow agents on a piece of the Death Note by threatening Raye's family. Because of the simultaneous death of these twelve FBI agents in Japan, including Penber, the police are scared to continue investigating, and the American president pulls the FBI off the Kira case. The Japanese police, who were previously unaware that there were FBI agents in Japan, conclude that L hired them to investigate the Japanese police and their families, causing them to distrust L. Soichiro announces that because of the heightened stakes of the case, any officer who no longer wishes to work on the Kira investigation may leave, and will not be demoted for doing so. Only five officers decide to remain on the case. In an effort to repair his relations with the Japanese police, L meets in secret with the remaining detectives who want to work on the Kira case.

In his meeting with the detectives, L reveals his thoughts about how Kira might be following the murders of the FBI agents and pinpoints who the federal agents were tracking during that period.

Light writes the name Shoko Maki on the Death Note. Just before the Death Note takes effect, Light informs the victim that he is Kira. Meanwhile, Watari reveals his identity in the meeting with Light's father and the other detectives. He gives the detectives special gadgets embedded in clothing in the event Kira comes into contact with them or they are in trouble. Detective Shuichi Aizawa is sent to the police headquarters by L.

L is close to discovering the identity of Kira. He requests surveillance equipment to be installed in the homes of those he suspects, including Soichiro Yagami's son. Light, however, becomes aware that he is being watched and has Ryuk locate all the cameras in his room. He deceives the surveillance team by watching the news on a portable television hidden in a bag of potato chips and continues to kill the criminals being reported.

L's suspicions are momentarily subdued, but he does not discard the possibility that Light may be Kira and decides to meet him in person. At the college entrance exams, Light notices a mysterious and eccentric student staring at him, who introduces himself as Hideki Ryuga, the same name as a famous idol. Light is shocked when "Hideki Ryuga" reveals himself as L. Since Light risks either killing the real Ryuga by accident or arousing suspicion by having L die right after meeting Light, he decides to befriend L, gather more information about his true identity, and kill him at a later time.

In a bid to profile Light's behavior, L challenges him to a game of tennis. L asks him some questions regarding the Kira case and invites him to help in the investigation. The two then receive news that Soichiro Yagami has had a heart attack and is in the hospital. Light promises to his father that he will make sure Kira is caught and executed for making him suffer. On the way out, L confronts and scrutinizes Light, still uncertain whether or not he is Kira. Light attempts a bluff and demands to be placed in a prison cell without television for one month to prove his innocence. L is satisfied but curious that Light should offer this proposition. Meanwhile, television station Sakura TV receives audio tapes from an anonymous person claiming to be Kira.

Sakura TV is forced to broadcast several prerecorded audio messages allegedly from Kira. L determines the messages are trying to gain public support for Kira and must be stopped, but the investigation team are unable to contact the station directly. Hirokazu Ukita, one of the investigators working with L, rushes to Sakura TV but mysteriously dies in front of the station, along with two police officers. The investigation team believes that Kira no longer needs to know the person's name to kill, while L suspects this may be a new, different Kira. Soichiro Yagami, hearing news of the broadcasts, hijacks a bus and crashes into the Sakura TV lobby to avoid being seen while seizing the Kira tapes. With the police and the investigation blocking any view of his face while leaving, Soichiro brings the tapes back to the investigation team headquarters. A young girl named Misa Amane discusses her admiration for Kira with a shinigami named Rem, and reveals that she has made the trade for shinigami eyes.

Light meets with L and the detectives. To test Light's analytical skills, L has him listen to the recordings confiscated by the team to determine if there are any clues in the reader's voice. In this way, L concludes that Light cannot be Kira. The team then broadcasts a recording made by L and Light to trick the second Kira into replying. Shocked and wanting to pursue this lead, the investigation team formulates a plan, while Light decides what to do.

Detective Touta Matsuda and Light volunteer to go to Aoyama to investigate on the date mentioned in the journal entry. Light intends to find out who the second Kira is, and in order to keep his identity unknown to the shinigami following Misa, he gets a group of his friends to surround them while they walk. Possessing the shinigami eyes, however, Misa finds out that Kira is Light Yagami because, as a Death Note holder, his life span is the only one she can't see. Later, Misa confirms to the investigation team that she has found the real Kira. The team decides to change their approach and try to reason with her. They release a television broadcast condemning Kira as a heartless murderer who will kill anyone who discovers his identity. Furthermore, they offer to lessen the severity of the punishment the second Kira will face if she reveals information about the real Kira. Misa ignores this, finds Light and explains that she tracked him down because she loves him.

After Light introduces Misa to Ryuk, the two discuss their plans to get rid of L. Taking advantage of the situation and of Misa's love for him, Light concludes that he can use her to mislead L, while furthering his plans for a better world. Misa's shinigami, Rem, however, threatens to write down Light's name in her own Death Note if Misa's safety is compromised. In the meantime, L is thrown off the trail by the second Kira and is confused by the new audio tapes purposely denouncing the police's attempt to make the first Kira appear as a pariah. L concludes that the two Kiras might have met and are working towards the same goal.

Worried at the prospect that he might be murdered, as he is convinced the two Kiras have met, L demands that in the event of his death, Light should be arrested. Later, Light and L meet each other outside college. Much to the anger and frustration of Light, Misa appears and converses with the two. Minutes after Misa leaves, Light receives the news from L that she has been arrested on grounds of being the second Kira. Misa appears to be blindfolded and tied to a chair, while L instructs Watari to torture her to obtain information. A few days later, Misa relinquishes ownership of her Death Note, thus erasing her memories of its existence.

Light decides to tell L that he thinks that he may be Kira subconsciously and wishes to be confined. Light's father also believes it is a good idea that he himself be confined to a cell as he cannot risk his emotions getting the better of him in this investigation. Light concocts a plan whereby he tells Ryuk he will relinquish ownership of the Death Note at any time in a discreet discussion, while being monitored by L. After Light's imprisonment, Kira's executions stop and L's suspicion is heightened. Light chooses this time to give up the Death Note, losing his memories of being Kira. His change in behavior puzzles L; Light goes from being calm to completely desperate. The Kira executions then resume and the new spate of killings confuses L.

In a last bid to determine if Light and Misa are the two Kiras, L and Soichiro stage a stunt in which Light's father attempts to kill Light and then himself out of shame. Seeing Light and Misa's reactions to it, L intervenes and announces that he no longer suspects them of being Kira, although he is still suspicious over the fact that Misa's DNA was found on the audio tapes. Misa is released, but Light continues working on the Kira case. L and Watari move the investigation team's headquarters to a new building inside the city. Elsewhere, Rem speaks to a mysterious businessman about the Death Note. Eight businessmen then plan the next murder Kira will commit in order for the Yotsuba Group to excel in the market.

L proposes that he be tied to Light, causing a scuffle to break out in the new headquarters. It is some time until Kira begins killing again, which has L and Light thinking that Kira may be killing for monetary profit. Their investigation leads them to the Yotsuba Group, a rich organization that dominates global markets. Kira is also reported to have been sending threats to politicians and the investigation team is forced to conduct their operations in secret. Aizawa quits the Task Force, angry at L for testing his loyalty, although he feels conflicted about his decision. L brings two new members to the investigation team, Aiber and Wedy.

Feeling inferior at his lack of participation in the Kira case, Matsuda decides to snoop around the Yotsuba Group and do his own research. He finds evidence that Kira is in the building, but is apprehended by the eight businessmen before he can act. Using the fake identity card Watari gave him, he passes himself off as Misa's manager. He pretends to offer a deal involving her in their commercial campaign, while contacting L using his modified belt buckle. Following L's instructions, he then fakes his own death. In one of the Group's later meetings, one of its members chooses to leave out of fear he may have to face the consequences of Kira's actions.

The investigation team installs wiretaps and surveillance cameras to monitor the Yotsuba Group meetings and are amazed at how openly they discuss their use of Kira. Light and L come up with a plan to contact one of the members of the Group, Reiji Namikawa. Namikawa agrees to act as a spy and help postpone Kira's killings by discussing them at the meetings. L reveals that he still suspects Light is the first Kira by playing mind games with him. Afterward, L questions Misa and wants her to infiltrate the Yotsuba Group to obtain information. Soichiro worries that even if they do gather enough information on the Group it will be difficult to capture all of its members at the same time.

The third Kira sets his eyes on Misa after meeting her. While Misa is taking a break from meeting with the Yotsuba Group, Rem contacts her. Misa is able to see the shinigami, but her memories of being the second Kira do not return upon touching a portion of the Death Note that Rem has brought her. Rem then tells Misa about everything that has happened and that she must trust Light lest she be killed. Upon re-entering the room, she spots who the third Kira must be: Kyosuke Higuchi. Misa goes on a date with him and is able to obtain proof that Higuchi is the criminal L is looking for. Her ease in determining who Kira is leaves L very suspicious, since he could not deduce it himself.

After learning that Higuchi is Kira, L decides that the police must not apprehend him until they understand his killing method. He arranges for Sakura TV to air a "Kira special" where Matsuda will declare he knows the identity of Kira to lure out Higuchi. Having been granted immunity from prosecution, several of the businessmen trick Higuchi and lead him to follow L's plan. As the third Kira races to the television station, determined to kill the whistleblower, L and the investigation team watch his every move via cameras and wiretaps.

While driving to Sakura TV, Higuchi talks with Rem about his situation. L, Light and Misa watch from the investigation team building and wonder who he is talking to. L wonders if Higuchi is talking to a shinigami. Higuchi enters the station's offices and writes Matsuda's fake name in his Death Note. The team thinks he has just written a note to himself, but find his subsequent erratic behavior odd. L argues that Higuchi has attempted to use his killing method. Higuchi then makes the deal with Rem to obtain shinigami eyes. A furious pursuit ensues when L realizes Higuchi can kill after looking at a person's face and orders the police to apprehend him. Aizawa and Ide return, leading a squad of police cars to block Higuchi's path. After this, Aizawa rejoins the Task Force.

Higuchi is arrested on grounds of being Kira and causing multiple murders in the region of Kanto. After inspecting Higuchi's Death Note, L discovers that shinigami do exist. While L is stunned, Light takes the Death Note from him and remembers that he is the original Kira. Light then kills Higuchi by writing his name on a scrap of the Death Note. It is revealed that when Light gave away his Death Note, he added a fake rule stating that, after having written in the book, its owner must continue to use it at least once every thirteen days or perish. The investigation team reviews the rules written in the book and finds that they can do little to get rid of it. Meanwhile, Light orders Misa to recover the other Death Note he had hidden a few months earlier. Having lost her shinigami eyes when she relinquished her Death Note, Misa makes another deal with Ryuk in order to find out L's true identity.

L asks Rem about Death Notes; she reveals as little information as possible to avoid implicating Light or Misa. Meanwhile, Misa begins to use her Death Note to kill criminals. Although Light denies Misa's involvement, L becomes very suspicious of her and Rem realizes that it was Light's plan all along to endanger Misa so that Rem would sacrifice herself to kill L. Later, Light finds L on the roof of the investigation team headquarters. The latter laments how distant he is from other people and how often they, like most people, lie. When the two rejoin the rest of the team, L reveals that he is planning on testing the thirteen-day rule, the only thing currently absolving Misa. Before he can do so, however, Rem kills Watari and L at the cost of her own life. After secretly snatching away Rem's Death Note, Light celebrates his victory in silence.

The first half of the episode features L narrating the events of the first 25 episodes. The account of the Kira case is revealed to have been left behind by L as a record of his achievements as a detective. It is deleted by Light when he discovers it. The investigation team appoints Light as L's successor and agrees to not publicly announce L's death. Light resumes his executions with a vengeance, killing Aiber, Wedy, and the remaining Yotsuba group. The show jumps ahead in time five years, depicting Light joining the National Police Agency (NPA) of Japan in 2012, at the age of 23. Five years earlier, shortly after L's death, L's computer is shown automatically notifying an elderly man of L's fate. The man then reveals this information to two children.

Orphanage caretaker Roger Ruvie informs L's successors, Mello and Near, that L has died. Relinquishing the opportunity to succeed L, Mello leaves the orphanage to pursue Kira on his own, backed by the American Mafia. Near allies himself with the President of the United States. Along with Steve Mason of the FBI, he forms an organization whose goal is to catch Kira, the Special Provision for Kira (SPK). Aizawa informs Soichiro that the director of the NPA has been kidnapped and demanded the Death Note under Light's task force's possession as ransom. They don't know this yet, but it was Mello who kidnapped the director. As soon as Light discovers this, he kills the director. Mello then decides to kidnap Light's sister, Sayu. While scrambling to find a way to rescue Sayu, the investigation team contacts SPK for help in solving the case of kidnapping. This is where Near reveals that he knows of L's death and that someone has attempted to replace him.

Near suggests that he and Light cooperate to rescue Sayu. Soichiro takes the Death Note to the exchange point chosen by the kidnappers in Los Angeles, but Mello's men hijack the plane he is on and drop him off in the middle of the desert. Light monitors his father via satellite, until he enters an underground facility. There, Soichiro exchanges the Death Note for Sayu. Mello slaughters most of the SPK once he obtains the Death Note. Near then proposes to Light that the two cooperate completely in the future, and shares his suspicions that Mello is playing a game to see who can catch Kira faster. Meanwhile, in the shinigami realm, a shinigami named Sidoh tells another, Armonia Justin, that he lost his Death Note. Justin informs him that it was stolen by Ryuk and dropped in the human world.

Light uses the Death Note to have a member of Mello's Mafia mail him the address of their hideout. Sidoh sees the address and goes to find Mello, revealing to him that the 13-day rule is fake. Meanwhile, Light informs Ryuk that he will give up ownership of his Death Note and borrow Misa's. The next day, Misa, posing as Kira, calls the investigation team to tell them that she will give them her Death Note. She also tells them that most of the members of Mello's mafia will die on November 10 and that will be the best time to find the stolen Death Note. Upon receiving the second Death Note, Soichiro makes the deal with Ryuk to obtain shinigami eyes. The investigation team storms Mello's facility on the set date. Soichiro comes face to face with Mello and reads his true name: Mihael Keehl. Before he can write it on the recently recovered Death Note, however, Soichiro is shot. Mello escapes by detonating explosives and Soichiro is taken to a hospital, where he dies comforted by the belief that his son cannot be Kira because he can see Light's lifespan. Light returns Sidoh's lost Death Note to him.

The President of the United States declares America's neutrality regarding Kira in Sakura TV's program Kira's Kingdom. Meanwhile, a scarred Mello uses SPK agent Halle Lidner as hostage to gain entrance into Near's headquarters and meet with him. Mello wants the picture Near has of him so that he will remain safe from Kira. In return, he tells Near about shinigami and that some of the Death Note's rules are fake. Already suspicious of Light, Near proposes to the investigation team that they test the "thirteen-day" rule, but none of them believe that they should. In response, Light contacts the President of the United States, asking for information on the whereabouts of the SPK and threatening to kill him if he does not cooperate. Aizawa, who has started to suspect Light, considers informing Near. Later, Hitoshi Demegawa, the host of Sakura TV's show, goes to America as Kira's messenger and gives a worldwide broadcast inciting people to break into the newly found headquarters of the supposedly evil SPK.

Demegawa commands Kira's followers to break into the SPK headquarters in New York, while Misa watches the scene on television, waiting to kill Near as soon as he exits the building. Near asks the Japanese investigation team to consider that Light may be Kira. He and the remaining SPK members then escape the building by dropping buckets of money out of the windows to distract the protesters. Aware that his team is beginning to doubt his identity, Light e-mails Misa with a new plan. Aizawa offers Near information about the past investigation that leads him to conclude that Light is Kira. Aizawa then tells Light that he would like to resume surveillance on Misa and him to help clear their names, to which Light agrees. Demegawa appears on television soon after, asking Kira's followers to donate money to build a temple to worship Kira. Disgusted, Light has Teru Mikami, the new owner of Misa's Death Note whom Light selected based on his appearances in Kira's Kingdom, kill Demegawa. Back at the investigation team headquarters, Aizawa realizes that with both Light and Misa under observation, the new killings cannot be attributed to either of them.

Tragic events in Teru Mikami's childhood convince him that God wants him to stand up to evil. As a result, when criminals everywhere begin to die, Mikami believes that this is God's righteous judgment and becomes a frequent guest on Kira's Kingdom. After Light gives him a Death Note, Mikami becomes ecstatic and passes judgment on criminals in Light's stead. He chooses a new spokesperson for Kira: Kiyomi Takada, who happens to be one of Light's girlfriends in college. Light realizes that he can use this connection to his advantage and sets up a meeting with Takada, ostensibly for the benefit of the investigation. While the two meet, Takada receives a call from Mikami and Light reveals himself to Mikami as Kira. They create a ploy to force the investigation team to remove all bugs from the room, after which Light tells Takada that he wants her to be his goddess in the new world. Light then tells the investigation team that he will pretend to be Takada's boyfriend to catch Kira. Elsewhere, Mello watches Misa, suspecting her of being the second Kira.

Near goes to Japan, allegedly as bait for Kira, and ponders on how to beat Light, knowing that the one who is doing his will has shinigami eyes and that the two communicate via Takada. Following Light's instructions, Takada asks Mikami to send her five pages of the Death Note. She tells him that he will continue his work in a fake book made to look like the real one. While walking to a broadcast, Misa runs into Takada and rushes her, jealous that she is not the most popular star. Halle Lidner, who has been sent by Near to act as Takada's bodyguard, stops her, but Takada meets with Misa for a girl-to-girl talk soon after, with Lidner sitting in with them. By the end of the conversation, Takada is convinced that Misa is stupid and Lidner reports to Near about the love triangle between Light, Takada and Misa. Elsewhere, SPK member Stephen Gevanni confirms that Mikami is the new Kira, after watching him kill a man by writing something in a notebook.

After Gevanni's report, Near decides that they must get close to Mikami discreetly, so that the shinigami trailing Mikami will not warn him. Meanwhile, Aizawa marks several notepads before Light and Takada meet, to determine whether or not they are communicating in secret through written notes. Takada tells Light of her meeting with Misa. Annoyed at the trouble that both women cause him, Light assures her that she is the only one for him. He then writes a script for Takada that makes it sound like she has agreed to help capture Kira. After the meeting, Aizawa's suspicions are confirmed. The SPK picks up Misa then and, when Light contacts Near to tell him that they have lost track of her, Near informs him that he has her. Meanwhile, Gevanni searches Mikami's gym locker and finds the notebook. During a second visit, Gevanni takes photographs of the names written in it. Near determines that the handwriting is Mikami's. Now having everything he needs, Near sets his plan in motion.

Each having developed a strategy to bring the other down for good, Light and Near finally meet face to face in an abandoned warehouse. Light brings out Mikami to have him write the names of everyone but Light on his Death Note. Meanwhile, Near is confident that the pages of the notebook Mikami is using are fake, revealing that he has tampered with them. All they need to do now is check whose name was not written to find out who the real Kira is. Light struggles to mask his glee as he thinks of how he already knew of Near's actions and that that had been why he had Takada keep the real Death Note while switching Mikami's with a false one. As the seconds before the Death Note's power takes effect count down, Light declares his victory to Near.

Mikami's Death Note fails to work. Near reveals that he knew about the fake notebook and had actually tampered with the real one. Mikami is restrained and, faced with Near's undeniable evidence, Light confesses that he is Kira. Light then attempts to write Near's name on a piece of the Death Note hidden in his watch, but Matsuda stops him by shooting him several times. Seeing Light writhe on the floor in agony, Mikami kills himself, causing a commotion that allows Light to flee the warehouse. However, Light's wounds do not allow him to travel far and Ryuk, reasoning that Light will offer him no further entertainment in defeat, writes down Light's name in his Death Note, just as he promised when they first met. Light dies of a heart attack, seeing L's figure in front of him.