This is from a strategy guide I wrote back when I first joined Particle Systems:
Objective 3: Disable LDS field generator
Byrne says the Megatransporter’s shield and LDS drive are being projected from an aft unit. You won’t be able to blow up the Megatransporter until this is destroyed.
Destroying it is tricky. Moving around in the LDS field is difficult, and the transporter will keep on turning to keep its rear away from your guns. Also the Megatransporter has a very powerful PBC turret at the rear. Missiles don’t work properly in the LDS field, so don’t use them.
To destroy the shield and LDS drive, target it (It’s called CABOOSE), fly round to the rear and attack it with rapid fire PBC blasts. When the transporter turns, it normally turns in one direction, keep moving on the inside of the turn to keep the rear in view, shooting at the rear whenever you can. When you destroy the LDS drive the ship will drop out of LDS, and start launching tugs.
Objective 4: Destroy Megatransporter
Try to concentrate on destroying the Megatransporter. Ignore (if you can) the tugs for the time being. If you don’t destroy the Megatransporter quickly you’ll find it difficult to get a clear shot at it as it will keep launching more and more tugs.
Get close enough and you can subtarget one of the pods on the transporter. Shoot this with rapid fire PBC and you’ll destroy the transporter very quickly, otherwise it’s very well shielded and will take a while to destroy.