In this mission, you have to destroy F.A.T.H.E.R. completely.
It is a good idea to start by destroying all the extra power supply, flak towers and other nonessential things on the tech island to save money. Your combat fleet will be expensive. Note: Despite the fact that they say "you have been given command of the unified armed forces", they will not give you a fleet, you have to build it yourself.
You already have an EMP, but build more, if you lose it you will not be able to attack his ark and units,
F.A.T.H.E.R's vehicles that have unique names are invincible.
F.A.T.H.E.R's vehicles that are named after their unit type are not invincible.
F.A.T.H.E.R's Ark is capable of spawning Deep Sea Hunters, invincible Choppers, and invincible Vipers although the total number of invincible units he can have (when none are disabled from EMP) seems to be capped at 4.
Optional Mission: Shields Up
- Click on Yana Rodriguez's Ark to contact her.
- Destroy F.A.T.H.E.R's Airport.
- Pick up the “Shield Transformer” item from the ocean and bring it to your Tech city.
- Build 1 Generator and 1 Filtration plant at your Laboratory.
- Research “Optimized Projectile Barrier” under the Units category at your Academy.
Optimized Projectile Barrier gives all your vehicles +500 shields and +500 shield regeneration when socketed in your Ark.
Optional Mission: With Own Weapons
- Click on Rufus Thorne's Ark to contact him. (ignore the mission text Thorne gives you. It is incorrect.)
- Destroy F.A.T.H.E.R's Shipyards.
- Pick up “High velocity projectile” from the ocean and bring it to your Tech city.
- Build 1 Generator and 1 Impact booster at your Laboratory.
- Research “Universal Precision Strike Guns” under the Units category at your Academy.
Universal Precision Strike Guns gives all your vehicles +15% attack when socketed in your Ark.
Optional Mission: Unseen
- Bring Omega Team in a submarine to the underwater warehouse behind F.A.T.H.E.R. without being detected by scanner units.
- Bring “Optical fiber” back to your Tech city.
- Build 1 Generator and 1 Metamaterial at your Laboratory.
- Research “Cloaking Field Mk IV” under the Units category at your Academy.
Cloaking Field Mk IV cloaks all vehicles near the vehicle that has the item equipped.
It is possible to buy a hijackers item from Rufus Thorne and capture F.A.T.H.E.R's invincible ships to use for yourself. F.A.T.H.E.R's ships are equipped with the item “Projectile barrier AT-5”, which adds +15,000 shields and +50,000 shield regeneration (yes, you read those numbers right). After capturing one of his ships you should move this item onto a different vehicle, as F.A.T.H.E.R's units are invincible even without it.
Defeating Father: The Final Battle
In order to damage F.A.T.H.E.R. you will first need to use the EMP Cannon on his Ark. Keep all of your other vehicles at a distance so none of them get caught in the blast. Then proceed to destroy all of the small turrets on top of F.A.T.H.E.R's Ark, before finally attacking F.A.T.H.E.R. Retreat whenever F.A.T.H.E.R. regains his shields. There is a timer in the upper left corner of the screen to tell you when this will happen. Repeat your attacks until F.A.T.H.E.R. is destroyed.