The Mantidox fleet engines were destroyed when the things that are they are coming fired upon the fleet. But the General had heard of the Doctor and began to set a trap.
The trap involved UNIT, the TARDIS' chameleon circuit and, not known to the Doctor, part of the d****s plan.
When The Doctor Came Calling
The plan worked and the Doctor soon came and was willing to help them, but UNIT had other plans. The two strike forces (one with Colonel Mace the other with General Akanzay) were both failures. Resorting to war, the Mantidox, now with fuel, planned to attack, but that never happened. As Paris started to burn Tom pressed the (very handy) self-destruct button which (also very handy) destroyed the fleet under Paris.
The Mantidox were at heart nice and friendly... not! The brutal and war loving Mantidox attack planets by tricking them into thinking they were peaceful. The inhabitants of those planets died.
- They shall return in episode 7.