Other grounds that support the views that the mastermind of the plot was the Imperial Court are that, after the Battle of Yamazaki, Nobutaka ODA tenaciously searched for Sakihisa KONOE by issuing an order to track down and dispose of him, that Kanemi YOSHIDA was interrogated for information, and that the original contents of "Kanemikyo-ki" (diary of Kanemi), which is the first class historical material for that time, were missing for approximately one month around Honnoji Incident and the section for 1582 was rewritten.
また、山崎の戦いの後、織田信孝が近衛前久に対し追討令を出して執拗に行方を捜したこと、吉田兼見が事情の聴取を受けていること、更に当時の一級史料である『兼見卿記』（兼見の日記）の原本内容が本能寺の変の前後1か月について欠けており、天正10年の項目は新たに書き直していた、という点も、朝廷黒幕説を支える根拠とされている。