Oh, dude, Nathaniel totally "died" in the Bartimaeus Trilogy. But like, he kind of didn't really die-die, you know? It's all like magic and djinn stuff, so it's not your typical RIP situation. So, technically, yeah, he "died," but also not really. It's all just a wild magical ride, man.
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In the Bartimaeus Trilogy by Jonathan Stroud, Nathaniel does not actually die. At the end of the series, Nathaniel sacrifices himself to save Kitty and Bartimaeus from Nouda, a powerful spirit. However, his essence is preserved within Bartimaeus, allowing him to live on in some form. This act of selflessness and sacrifice demonstrates Nathaniel's growth and redemption throughout the series.
Well, honey, Nathaniel did kick the bucket in the Bartimaeus Trilogy. He met his end in the third book, "Ptolemy's Gate," sacrificing himself to save the day. So yeah, he's pushing up daisies in the magical world of Bartimaeus.
It is uncertain whether or not he did die, and in fact his absence suggests that he might have. However, it is mentioned in one of the earlier books, Amulet of Samarkand I think, that sometimes a spirit who has been imprisoned for a long period will grant a favor or favors to the individual that freed him. Under this rule, there is a possibility that the two that were in the staff may have protected or spared Nathaniel in gratitude. But then again, they could've been some of the more ill-spirited types and could've killed him. Up to the reader to decide I suppose.
Nathaniel Spence died in 1914.
Nathaniel Allison Murray died in 1959.
Nathaniel Fillmore died on 1863-03-28.
Nathaniel Alexander - bishop - died in 1840.
Nathaniel Gottfried Leske died in 1786.