-[ ALL SHIPS ]-
You still need Energy Skeeters, so don't remove them!!
-[ Angelwing ]-
Swap 3x Plasma Cell for 3x Crystal Cell, and anything else you want. You need Commandos, so make sure you have them ON the Angelwing!
-[ Brutus ]-
Swap 1x Volcano Plasma Gun for 1x Nova Plasma Gun, 2x Plasma Cells for 2x Crystal Cells
-[ Sparta ]-
Swap 1x Volcano Plasma Gun for 1x Nova Plasma Gun. Add anything else you want.
-[ Avalanche ]-
Swap Fusion Engine for Antimatter Engine, 1x Bubble Energy Shell for 1x Delektron Shell, and whatever else you want.
-[ Guardian ]-
Swap Fusion Engine for Antimatter Engine, add L2 Quark Support Generator, add 1x Plasma Cell
-[ Colossus ]-
Add Torsion ECM System, 2x Delektron Shell
We have a few things to do here. We must deploy four Blocker Generators so we can kill the Entity Sphere. Plus, there are some infected ships floating around that we need to deal with, and, a friend of ours is out there, too. And we need to save him.
First, decloak. Being cloaked is worthless. Set all ships to defensive. Set the Ghost Ships shields to 200% and the Angelwings weapons to 200%. Now head to Deploy Point 2. Have the Ghost Ships guard the Angelwing for now.
There are 5 ships in this area, three cruiser-class ships: Sentinal, Hacker and Keeper. These guys are more annoying than anything. There are also two battleships, the Balthasar and the Rampart. These ships are all infected and are hostile! Do not hesitate to destroy them!!
On your way, the Sentinel will show up and start harassing you. Kill it. Deploy the Generator (just get to the deploy point, it's automatic from there). Once you're informed that it has been deployed, head for the next closest one.
The Hacker and Keeper are still left, both are Cruisers. If you encounter them, kill them. You'll also find out that the Balthasar is here (Admiral Norbank) and there's one other battleship, the Rampart. Try to destroy all the other ships before messing with the Balthasar.
Thankfully, the Balthasar has no Flak guns, so all we need to do is drop its shields and send in our Commandos. Use the Ghosts to attack the shield device while the Angelwing hammers with the Delektron Shells. Once the shields drop, send in the Commandos and rescue the Admiral. Once they return, destroy the Balthasar and any remaining infected ships.
Once that's done, head to the rest of the Deploy Points and deploy the generators. When you've deployed them all, your fleet will warp in, along with the Exterminator, a battleship.
Now, select EVERY ship and have them use their Energy Skeeters on the Entity Sphere. Make sure they're not firing any other weapons as they'll recharge the Entity. Once you destroy the Entity...