In the following year, 1600, Ono Harunaga joined forces with the Eastern army at the Battle of Sekigahara and distinguished himself in battle, thereby earning a pardon for his crime from Ieyasu. Following the battle, under orders from Ieyasu he bore a note from Ieyasu to the Toyotomi clan, in which Ieyasu declared, 'I bear no animosity towards the Toyotomi clan' after which he remained in Osaka and did not return to Edo.
In 1615 during the summer campaign of the Siege of Osaka, Harunaga sent Senhime (daughter of Tokugawa Hidetada and Hideyori's wife) as a messenger for Ono, to plead for clemency for Hideyori and Yodo-dono, on the condition that he commit ritual suicide, but subsequently he and Hideyori committed suicide in a mountain hamlet in the vicinity of Osaka Castle. He died at the age of 47.
Records show that rumors abounded throughout the Edo period regarding Harunaga having an adulterous affair with Yodo-dono, and some accounts maintain that Hideyori was not a biological child of Hideyoshi, but of Harunaga and Yodo-dono. As described above, because he was a foster brother to Yodo-dono, it is likely that their relationship was extremely close; however, with the decline of the fortune of the Toyotomi family and the accompanying 'futility of ruin,' it can also be thought that the rumors of the sin of adultery were created with a view to casting him as an evil person (from a Confucian sense of resignation).