When Callufrax Minor was stolen from time by the Daleks and pulled into the Medusa Cascade, Es'Cartrss somehow made it to the Crucible, unnoticed by both the Daleks and the allies of the Tenth Doctor. When the Daleks were defeated, he was also able to escape into the Doctor's TARDIS. When the Doctor was alone, Es'Cartrss attacked, attempting to take over his mind. The Doctor's link with the TARDIS saved him and in an attempt to fight back, they were all pulled into the TARDIS' Matrix.
Within the Matrix, the three minds were able to form a world, creating a museum based on the Doctor's past. Es'Cartrss took the form of the Meta-Crisis Tenth Doctor and called himself the Valeyard, while the TARDIS initially took the form of Martha Jones. Es'Cartrss tried to steal the Doctor's memories, while the TARDIS helped the Doctor regain them. The Doctor was eventually able to regain all his memories and confront Es'Cartrss. Using the memories and will-power from his previous regenerations, the Doctor was able to take back the Matrix and seemingly kill Es'Cartrss.
Es'Cartrss had in fact managed to remain in the TARDIS vortex for years until it was expelled into E-Space when the TARDIS exploded. Eventually, the entity joined with Sondrah, an auditors of a race called the T'keyn and attempted to take revenge on the Eleventh Doctor by putting the Earth on trial in the late 19th century. Defeated in the trial, Es'Cartrss, still in its host body, was apprehended by the T'Keyn and was last seen swearing further revenge on the Doctor as it was being taken away. (COMIC: Dead Man's Hand)