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Later in the anime we discover that the calamity didn't start when Kouichi joined, but rather in April when Misaki, the twin sister, died from leukemia.

My question is what caused the calamity. Was it because Mei and Misaki were secretly talking to each other? Or was it because the students were confused and mixed Mei with Misaki?

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It's neither.

The Calamity is the Curse on class 3-3 where someone who is supposed to be dead joins the Class and this causes members of the class and their families to be killed off until the end of the year or the Calamity is stopped prematurely.

Because of the unnatural presence of this dead person walking amongst the living, at least one student from class 3-3 or one of their family members or the teacher of the class dies each month. At the end of the school year, the Extra simply disappears, the Calamity's effects on the class' memories and physical records are reversed, and the survivors forget that the Extra was ever part of the class. The Calamity has run its course, thus marking an end to the deaths, until the next year. The reversal must not be entirely complete, since Chibiki has been able to record the Extra's name most years, after the fact.

Source: Class 3-3 > 1973 - The "Calamity" of Class 3-3 Begins (Last Paragraph)

The Calamity is the result of Class 3-3 of 1972 not accepting the death of a fellow classmate and acting as if they still were there. This invited the dead to the class and thus the class became closer to death itself. Starting from 1973, the Calamity would start on its own without anyone triggering it.

Misaki Fujioka's death therefore is the result of The Calamity and not a trigger for it, it is also a sign it started as she is a family member of Mei

[Misaki Fujioka] dies in Episode 1 from the 9th grade class 3-3 curse, being "the death of April", the first one who died because of the curse.

Source: Misaki Fujioka > Plot > Another (first paragraph)

While the various media differ in how she died (due to a kidney transplant, or due to her leukemia), they all point to her being the first death by The Calamity in 1998.

  • Sorry, my question wasn't clear. I was thinking about the charm, how was the charm broken before Kouichi joined? Because the calamity took it's first victim back in april, did the present class decided to put a charm after the death? Or did they put a charm at the beggining of the year, and somehow broke it? – Teo Apr 22 '18 at 16:07
  • @Teo what do you mean by Charm? you mean how Countermeasures's plan was to choose one student and pretend they didn't exist? – Memor-X Apr 22 '18 at 22:32
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I think that it was never the student's fault but rather the teacher's fault because class 3-3 had the correct amount of seats that year, and the missing seat was in the faculty room.

She also points out that their class was the only one to have an Assistant Homeroom teacher and that they actually had the correct amount of seats this year and the missing seat actually being in the faculty room.

Source: https://another.fandom.com/wiki/Mei_Misaki

So, for the charm to work, it would've been the teacher who had to be ignored and not a student.

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