Another 2001 is the name of the sequel novel set three years after the original that follows the new class 3-3 facing the curse.

It has been three years since the calamity of 1998 that claimed the lives of many students in Yomiyama North Middle's class 3-3. After being placed into the cursed class, Sou Hiratsuka will have to work alongside class of 1998 survivor Mei Misaki in order to avert a new disaster. But as mysterious accidents and deaths pile up despite their countermeasures, the pair will be forced to reckon with Yomiyama North's deepest mysteries...

A few days before he starts the first semester in his third year at Yomi North, Sou Hiratsuka moves into Unit E-9 in the "Freuden Tobi" apartment building. He has his own room, but lives under the care of Mr. and Mrs. Akazawa, who are his paternal uncle and his uncle's wife respectively. He feels anxious about starting a new year in the cursed class in the third year, Class 3, and wants to hear from Mei Misaki.

He receives a text message from his good friend, Nobuyuki Yagisawa, instead. Yagisawa shares that he is also feeling apprehensive, but is hopeful that the year will pass without any issues, and that the effects of the curse will not take place. Sou acknowledges to himself that, just because the last two years were "off-years" when the Calamity was not observed, this does not guarantee the safety of the upcoming school year.

He also reads a newsletter email sent by another one of his friends, Shunsuke Kouda, who along with Sou, is a member of the school biology club. Although Sou considers his late uncle Teruya to be his role model, and also has a passion for photography like Teruya did, Sou decided to join the biology club instead of the photography club.

Before going to sleep, Sou is surprised when he receives a notification of an email sent to him by Mei. In her message, Mei advises Sou to be careful as the new year is about to start. Sou resolves himself that whatever happens in the near future, he is the one who will have to take action.

He notes to himself that he had a similarly-odd experience sometime ago (during the events of Another S) where he wasn't quite himself, so he believes he is someone who would be capable of following through with being a non-exister. He also takes time to acknowledge who he is, the current date, and the fact that he is alive, seemingly to help him deal with the uncertainty regarding his mortality and who he was after the events of the previous novel.

The next day, it is the first day of the semester. Sou intentionally takes a while heading to class. He walks near the Yomiyama River when he encounters Yuika Hazumi. She calls out to him, and although Sou does not want to speak with her and tries to ignore her, she catches up to him and begins a conversation. Hazumi expresses her gratitude and thanks Sou for what he is about to do.

Later, after he arrives at school and enters the class, Sou observes his fellow classmates looking around nervously. He notices Yagisawa. A confident and clear-voiced student, who he later recognizes as Izumi Akazawa, suggests everyone should take their seats. The class teacher, Ms. Kanbayashi, then instructs the pupils to sit down after most of the students hesitate. He scans the classroom to see how many desks there are compared to the number of students. As Sou feared, there is one fewer desk available to use than there are students in the class. He nods to the teacher, and exits the school. He acknowledges that it's time for him to begin his role as a non-exister to help protect his classmates and their families.

In the evening, Sou runs into Izumi who lives on the same floor as him in the Freuden Tobi building. He notes that she is his cousin who must be around the same age as him. She helpfully provides him notes from the lessons he missed that day, and the two have a conservation about the risks and acceptable behavior that a non-exister should conform to. For example, the non-exister should not speak with their classmates during school time, nor should they be called upon by their home room teacher to speak in front of the class. It is considered okay, however, if a non-exister student communicates with their classmates outside of the school grounds when the school day has finished.

Sou is the protagonist of the novel, and majority of the story is told from his perspective. He finishes moving to Unit E-9 in the "Freuden Tobi" apartment building shortly before starting a new semester as a third-year student in Junior High School (equivalent to grade 9 in North America). For almost three years since September 1998, Mr. Akazawa (Haruhiko Akazawa) and Mrs. Akazawa (Sayuri Akazawa) have been taking care of him in their custody after he was driven out of his Hiratsuka family home.

Mr. Akazawa is the eldest of three brothers. The Freuden building is managed by Natsuhiko Akazawa who is the middle brother of Mr. Akazawa. Natsuhiko allowed Sou to live in one of the building's apartments since April. The youngest Akazawa brother was Hiromune Akazawa. Hiromune was Sou's father who had passed away 14 years ago, shortly after Sou was born. Sou's cousin, Izumi Akazawa, lives in another unit on the same floor as him.

Throughout the novel, when mysterious events take place or when certain memories are recalled, Sou senses an ominous feeling in the world around him as if things went pitch-black for a second and there was a "low, reverberating thumping just beyond [his] hearing", like a thud which he feels more than he hears. He has matured since the events of Another: Episode S, and often reaches out to Mei regarding the concerns he has and for advice on dealing with the unusual occurrences taking place.

He volunteers to be a "non-existing" student at the beginning of the school year, as planned during the strategy session that took place earlier in March with his classmates. As a "non-exister," his role was planned to counteract the presence of an extra person in the class who was secretly the "casualty." The "casualty" was a person related to Class 3 who had lost their life due to the calamity in a previous year, and who has somehow rejoined Class 3. Due to mysterious circumstances, other students and teachers cannot distinguish who the casualty is, since their memories of past years and even recent events are altered when the casualty joins the class. It's not logically explained how it works, but the majority of the records and documents about the school and Yomiyama's residents are somehow changed as well to omit details about the casualty's death. This makes it very difficult to identify who the casualty is.

Mei returns as another major character in this novel. She is now in senior high school and is 18 years old. Her role is somewhat reduced compared to the events of Another which took place three years ago when she was 15, but she remains to have a significant presence in the story. After experiencing the events that took place with Class 3-3 several years ago when she was chosen to be a non-exister, she has become wiser and more knowledgeable about the calamity and how to deal with it. She provides information and advice to Sou at multiple points in the story. She emails Sou at the start of his first semester in Grade 3 Class 3 and advises him to be careful.

Kouichi is on a trip abroad during the events of Another 2001. Despite being away from Yomiyama, he stays in contact with Mei through email or by phone. Later on in the year, he directly reaches out to Sou to give advice and try to help him deal with the strange events going on.

Nobuyuki Yagisawa is Sou's close friend. They had been in the same class for two years in Yomiyama North Middle School (called North Yomi for short), and are classmates in Class 3 together for their third year. Yagisawa is a cheerful and optimistic individual who tries to hide his fear about the rumors surrounding Class 3, even though the last two years were "off-years" in which no unusual events relating to the calamity phenomenon took place in the class.

Shunsuke Kouda is one of Sou's friends. He is the club president and Sou's fellow member of the school's biology club. Shunsuke was in Sou's class during the first year of middle school, and is also a friend of Yagisawa. He is a very meticulous and careful person.

Hazumi was in Sou's class in Grade 1 of Junior High School (equivalent to Grade 7 in North America). Hazumi and Sou were in different classes in their second year, before being in the same class in their third year: Class 3. She is a pretty girl who Sou describes as having delicate features and who acts grown-up and mature for her age. Despite this, Sou is generally cold towards her, and tries to brush off her attempts to be closer friends with him. She is about the same height as Sou.

She thanks Sou ahead of the semester for his offer to be a "non-existing" student, and she also becomes the second non-exister alongside Sou. Hazumi was selected in a lottery using playing cards as she drew the joker card which meant she was chosen. She feels hopeful and glad that Sou and her are working together in this situation. After some time, Hazumi becomes jealous of Sou's close friendship with Izumi, and later becomes unstable after feeling isolated and emotionally hurt by her classmates after several weeks of being a non-exister. She abruptly announces she no longer wants to act as a non-exister partway through the year which causes concern for Sou.

Izumi Akazawa is the cousin of Sou on his father's side. She lives in Unit E-1 on the same floor as him in the Freuden Tobi building. She was selected as the countermeasures officer at the strategy session in March, and is an articulate student who acts like a leader for the class. She likes to play piano, and she tells Sou how she wants to go to college and leave Yomiyama behind after she graduates.

Ruiko Etou is the student who suggested having two non-existing students to act as countermeasures to the casualty's presence in the class. She may have done so based on the information she presumably gained from her cousin, Haruka Etou, who experienced the events which took place in Class 3 in 1998.

In the novel, for the class of 2001, there were 19 deaths, as well as five more that were “unrelated” to the class. The total is 24 deaths.