Those were his remains. The Daleks exterminated him, and the Doctor put what was left in that box. However, his essence survived in a fluid-like form called either a morphant or a deathworm (See novel The Eight Doctors) His "last wish" was for the Doctor to transport his remains to Gallifrey; during transport, the Master was able to sabotage the Doctor's TARDIS, forcing it to land on Earth in 1999. The Master subsequently took over the body of Bruce, an ambulance driver in San Francisco. This incarnation was only intended to be a temporary one -- indeed, "Bruce" began to decay almost immediately -- as the Master launched a scheme to steal the Doctor's remaining regenerations.