Damn how do you complete the second part of Big Fish? I keep getting my ass handed to me
It's not too hard at all!. Took me just 5 attempts on a Beam-heavy Insane difficulty game.
AIM at the Hammerhead. LEFT SIDE. It only has light armour there and you can pierce it much quicker.
Pro Tip: Once the Hammerhead has been taken down, the enemy fleet retreats.
Setup with one Beam-heavy ship (or the Ion Cannons) to strip the shields off the Hammerhead. Crawler is your best bet here imo but any forward firing ship will do it (Right Hook and Big Bus are good)
Use two Colts as your sidekicks. Colt's are the best (heavy forward fire) and hook them up with the heaviest armour you can on their front. Their job is to strip armour and deal damage. I prefer 2x cannon and 1x beam with two boosters (cannon, beam or shield to suit you)
As soon as the Hammerhead warps in, go to Tactics and set both small ships to attack, follow them in hard and fast, strafe yourself around to aim up against their Left Side (preferably as it has light armour, sides and back have medium and front is heavy and silly).
I think you have about 90 seconds between the cutscene and your mothership being destroyed.
Further tips: Leech Beams might be useful to you as they drain the reactor of the Hammerhead, reducing it's damage output and keeping your ships alive slightly longer.
If you're speccing into cannons, Particle Cannons are going to be your saviour. Load up heavily on these and spray death.