Trench

From where you start there are flak shells on the left, and eightballs, an automag,
and a flak cannon, plus more, around the corner.
Head into the trench to fight another Titan. Kill him, carry on and kill the Skaarj
that you come to. Step into the pool of red light to lower a lift - this will gain
you access to the ship.
When you're inside, get on the next lift, go up, and go through the doors at the end
of the landing to progress further in the ship.