When the TARDIS was taken aboard a Sycorax spaceship on Christmas morning, he awoke with the help of some tea that seeped into a component of the TARDIS, (TV: The Christmas Invasion) alongside regeneration energy which he seeped from his third incarnation, who had arrived in Jackie's apartment moments before.
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The Doctor challenged the leader to a duel over the fate of Earth.
In the ensuing sword fight, the Sycorax leader chopped off the Doctor's hand.
He snapped out of it briefly to save Mickey and the Tylers from a Roboform Christmas tree, but the stress of waking up too soon made matters worse and he collapsed again.
He slept through much of the ongoing invasion by the Sycorax.
(TV: Time Crash) After the TARDIS became "stalled in the equivalent of a galactic lay-by", the Sixth Doctor had a worried thought of Peri Brown growing old and dying in the TARDIS, while he would "go on regenerating until all [his] lives [were] spent." (TV: Vengeance on Varos) When the Master exposed the Valeyard's alliance with High Council to the Sixth Doctor at his trial, he revealed that the Valeyard was acting as the prosecutor for the trial in exchange for the Doctor's remaining regenerations.