The time tunnel was retconned to be the Time Vortex that the Doctor threw Sutekh into at the end of their epic battle, but it was originally a separate entity. Sutekh was more than a stowaway ...
The Doctor uses a whistle to control his own TARDIS, firing a laser that destroys Sutekh's herald, Harriet Arbinger. He then ties Sutekh to the console and drags him into the time vortex.