So, are you a bad enough dude to rescue the president slaughter the Emperor's enemies? I'll tell you the best way to do this in the challenge mode.


Interceptors
Shields: You must have them as they are the only thing standing between you and getting one-shot by railguns. Not even Juggernaut + Carapace Armor would save you from that. Also, they recharge which armor cannot do.
AP Ammo: Makes you more effective against the big things you want to kill as this also effects your bombs. Two bursts of Purifier bombs will not kill a carrier unless you have AP ammo! Also, smaller stuff like fighters are already in OHK territory unless they have Juggernaut armor or shields for your...

Long Rifle: The ability to reach out and touch the enemy is something that you must have. It is OHK against fighters, 3HK against corvettes (with AP) and 4HK against heavy destroyers (with AP). So as a result you can make short work of enemy swarms or the escort of carriers. Furthermore, the ability to snipe off the torpedo turrets of carriers from a safe distance will make your life so much easier on your approach for bombing runs. You can also snipe out bridges or simply blast away at targets from max range if you'd prefer too. Don't be afraid to snipe flak or repair drones at range. However if the enemy has shields you are screwed unless you have....

Fury Missiles: Equal against shields and hull in practical terms this is what you will use to crack the shields for lighter enemies. If it's a fighter with shields, you can just dump the magazine and count it as dead. One magazine will take out the shields of a corvette or a heavy destroyer. You can also use it to finish off enemies, pop drones and even distract enemy omniflak from you as they will instead focus on the missiles.

Purifier Bombs: They're simply superior to the Scarab, so use these.

Destroyers
Shields: With shields your destroyers will be two-shot by railguns and Carriers have two railguns at a time. Do the math.
Shield Extenders: Your destroyers job is to (briefly) take the heat off you while they are alive. doubling their shields is the most effective way of doing this.

Torpedoes: Your only form of long-range (7km) shield damage that is actually worrying to a capital, you simply must choose this. They'll also handle all lighter targets well too.
Omniflak: When massed it'll slaughter fighters just as well if not better than the point defense and can shoot down torpedoes, the 2nd greatest thread to your capitals after railguns. A must take.

Frigate
Shields: Railguns are weaker to shields, and the frigate needs the leeway to do it's job. Regenerating HP is also always nice.
Repair Drone: For fixing your fleet up between waves, you only need one drone to do this.
Omniflak: For the same reason as destroyers. Keep your capitals lumped together and they'll live much longer!

Tactics:

• -If there is a wave with flak drones, snipe them ASAP. They will ♥♥♥♥ your interceptors up faster than you can blink.
  
• -Ditto for repair drones, but they are usually lower priority.
  
• -If fighting a Carrier wave (four Carriers), take out the carriers with railguns first as they are more dangerous to you than torpedoes that can only do 8.5km, which is much less than your 12km Long Rifle.
  
• -However if the Carriers have shields this is inverted. You want to take out the torpedo carriers with purifier bombs ASAP first, as they make approaching to under-shields range much more difficult than railguns.
  
• -Another tactic against shielded carriers is to "cross the T" or to attack aggressively from the front of their line as they warp in. The front carriers will block the railguns and torpedoes of the back carriers with their shields which will make your approach for a purifier bomb-run much easier. You should be able to take out one or two carriers in the first minute with this tactic.
  
• -Also, do not be afraid of sacrificing your interceptors to get fresh bomb reloads. As such try to only "graze" on escorts in carrier waves as needed so you have enough chaff to keep respawning. An exception to this is enemy frigates with torpedoes as they're simply too dangerous to your fighters. Eliminate them as soon as possible.