Here's a walkthrough I wrote way, way back when I first started at Particle Systems:

At all Costs

Objectives: Score:
1. Protect asteroid guns 350
2. Protect asteroid base 1450
3. Ensure destruction of Navy fleet 1200

Maximum Kill Bonus: 2000

Total: 5000

Special Ordinance Fitted: Double PBC
Remote Missile
Disruptor Missile

You must defend the guns against the Navy assault, and if you get the chance, attack the main Navy attack fleet. President King and his cruiser Excalibur are in the fleet, but if you get close, he escapes to fight another day.

Objective 1: Protect asteroid guns
This mission is one of the most difficult in the whole game. Yarwood radios that long range sensors have detected the Navy fleet, and it contains at least two Destroyers and a Cruiser.

The Indie base is defended by asteroid guns controlled by satellite relays, and you’ll see a HUD display showing the blue communication beams between the relays and the guns. If the relays go off line the guns are disabled, and the beams will disappear. You and your wingman, Last Ditch are defending the relays controlling the spider guns. The base has a limited amount of relays it can launch to replace those destroyed in action.

The Commonwealth Navy first sends some Patcoms to take out the satellite relays, while the capital ships hold position at a distance. DuBois says he sees the Patcoms, and there’s some troop carriers heading in as well.

Clays says that the transports are there to take out the guns when they go off line.

Note: It’s very, very difficult to protect all the guns. Do your best, but the key objective is to protect the base. If necessary forget the guns and try to destroy as many enemy ships as possible. You can lose several guns without failing the objective.

Keep close to the base. Don’t get distracted and fly too far away or you’ll fail the mission. Try to take out the Patcoms first, if possible. They are called Weasel 1, Weasel 2, etc. Target them with missiles and send your wingman to attack them. You probably won’t be able to prevent them taking the relays out, but it will keep them off your back while you take on the Transports.

Five transports are heading towards the spider guns. You can take them out in one of several ways. The easiest is to use your remote missiles. These will normally take out a transport in a single shot, but if you use all of the remote missiles on the transports you’ll find it difficult to take out the Navy capital ships later.

The other is to soften them up with missiles, then go in close with your PBC. Use the TRI to divert power to your PBC to kill them more quickly. You have to be fast about this, as while you’re taking out one the others will be attacking the other spider guns. The transports are very well shielded, so try to get your wingman to attack the same transport that you’re attacking.

Another way - though unconventional - is to ram them! The transports are vulnerable while they’re approaching the asteroids to dock. If you ram them using the instant shield (Keypad 0) you’ll at least knock them off course, and often you’ll either destroy them, damage them severely so you can cut them up with rapid fire PBC, or even cause them to crash into the asteroid gun and explode! If a transport can’t dock with a spider gun, it can’t destroy it.

Objective 2: Protect asteroid base
You must try to keep the Navy ships away from the base if possible. If don’t manage to defend the guns, or take too long the Navy capital ships along with numerous smaller vessels will close in for the attack. When too many ships get close the base will radio that it’s evacuating and you’ll fail the mission. When you’ve taken out the transports and Patcoms, head out towards the Capital ships.

Objective 3: Ensure destruction of Navy Fleet.
You can’t destroy the Cruiser Excalibur at this stage, as it’s too powerful. You can take out the two destroyers. If you have any remote missiles left use them on the destroyers. Keep your distance so you don’t get shot at and guide the missile in. One missile will severely damage a destroyer and sometimes destroy it entirely. Close in and finish off with missiles or PBC.

If you don’t have any remote missiles, then close in and use the Disruptor missile to deactivate the destroyers shield and guns. Subtarget the crew module and take that out with PBCs, then subtarget the thrusters or shields and take them out too. If you target the individual systems you’ll do more damage than shooting at the superstructure. When you’ve destroyed one or more of the destroyers the Excalibur will escape.

The Excalibur will launch some C-Fighters to cover its escape. They are difficult to kill as they are so manoeuvrable. Use the WEP console’s padlock view to track them so you can shoot them with PBC. If you have any missiles left use them on the fighters.

After you’ve got rid of the destroyers and the fighters concentrate on the remaining smaller Navy ships. Once these have been destroyed the Base will radio that the attack is over and the mission is successful.

Alternate Solution
There is a different way to complete the mission. At the start of the mission LDS to the vicinity of the destroyers and destroy them with remote missiles. When you’ve killed the Destroyers go back and take out the Patcoms, Transports and other ships using the techniques described earlier. You will likely lose most of the asteroid guns, but you will have protected the base from attack by the destroyers and should complete the mission.