Nagato dosent have anything that can destroy the Yata Mirror, WHICH repels
All attacks. (Thats clear as day) Nagato "Repeled AMaterasu off his body" But he did burn up, but he repeled it in time.
And he cannot survive Tsukiyomi, and defiantly cannot escape because you have to be an uchiha with a Sharingan, with the same blood within you as the User (Itachi)
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So if nagato get caught in Tsukiyomi it's basically over, unless itachi spare his life, (Like he did on kakashi)
The Totsuku blade is More than fast enough to Seal Nagato away Before he uses Chibaku Tensei. Chibaku Tensei takes like 5 minutes to gather up all the rocks, and ITachi can just Amaterasu the rocks or the Black Sphere. Or he Can just Seal him away While Nagato is Gathering up rocks, since the Totsuku balde Extends, And It's Fast.
And Nagato has nothing against genjutsu since jiraiya Got him on one.
So itachi would just kill him while he's under a genjutsu before he even Tries to escape it