The real IX was kidnapped by Xanxus, who had placed him within Gola Mosca, draining him of his life energy. When Tsuna sliced Gola Mosca's armor in half, the IX was able to use his flame to show Tsuna his past;the IX used to visit Tsuna when he was just a child.
In the future, he has been unaccounted for since the Millefiore Family raided the main Vongola headquarters. During Tsuna's training within Hibari's spiked ball, he appears in a vision with the other Vongola heads and is shown with a flaming scepter,his signature Dying Will Flame weapon. Seeing him in the vision causes Tsuna to believe that he may be dead. Like Tsuna and the first, the IX also knows how to use the Zero Point Breakthrough, using it to stop Xanxus' rebellion during the Cradle incident.
The Vongola IX's stamp is the Dying Will Flame; he marks documents with his flame, proving they are official.