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... naves, quae frumentum Tiberi subvecta[v]issent, onustae rudere decurrerent, aedificiaque...

Pluperfect subjunctive in historic sequence after "destinabat" replaces the fut. perf. indic. of the direct statement. Nero's words were "Naves quae Tiberi subvectaverint, onustae rudere decurrent." "[D]estinare" is followed by "ut" introducing a substantive (noun) clause equivalent to a noun as direct object.