Throughout Anime and Manga, there are always powerful characters who cannot be killed by logical means. The writer therefore has to come up with a plot device in order to have them killed.
Naruto: (There are a few examples in Naruto. I will only list some)
Itachi Uchiha: In order to kill him, Kishimoto gave him a vague, unexplained terminal disease
Minato Namikaze :He died before the story took place. However Kishimoto than made him very powerful. Therefore Kishimoto had to put him in a situation where he had to kill himself
Bleach
Ulquiorra Cifer: He was so powerful that he easily defeated Ichigo. Then Ichigo somehow came back to life in an OP Hollowfied form and ripped off Ulquiorra's arm. And then Ulquiorra disintegrated due to "internal injuries"

Hunter x Hunter (Later in the Manga)
There are many more examples. Have more Examples? Disagree with my examples? Let me know in the comments.
Naruto: (There are a few examples in Naruto. I will only list some)
Itachi Uchiha: In order to kill him, Kishimoto gave him a vague, unexplained terminal disease
Minato Namikaze :He died before the story took place. However Kishimoto than made him very powerful. Therefore Kishimoto had to put him in a situation where he had to kill himself
Bleach
Ulquiorra Cifer: He was so powerful that he easily defeated Ichigo. Then Ichigo somehow came back to life in an OP Hollowfied form and ripped off Ulquiorra's arm. And then Ulquiorra disintegrated due to "internal injuries"

Hunter x Hunter (Later in the Manga)
Neferpitou: (S)he was extremely powerful. Somehow Gon went into some OP super Saiyan form and killed him/her.
There are many more examples. Have more Examples? Disagree with my examples? Let me know in the comments.