Looks like I was too defensive. :)

do the following

Research the Anti Air Addon for the assault bots
** DO THIS FIRST **
Then build four Mass Extractors
(one with each of your starting engineers)
And two Power Generators and a Factory with your commander.
(All Upgrades ARE ALLOWED)
Once complete with upgrades order it to repeat build the assault bot only.
(do this for all future factorys)

Build one Factory for every mass point you have, adjacent is best as it provides good but limited and very much needed air cover.

With your first factory is complete build an additional 3x Power Generators
and 3x or 6x Research Stations, 6 can be tricky but if you are reclaiming the mass thrown at you by enemy units there is no reason you cant afford 6.

Once this is done research exclusively technology’s that improve your bots, Firepower and Health Armour and whatever else.

DO NOT BUILD ANY OF THE FOLLOWING:

Engineers
(Look after the four you got like they are your fingers
after all they pretty much are (with the commander being your thumb)
Other Mobile Units
Defensive Structures
Intelligence Gathering Structures (not needed anyway)
Air Factorys
Experimental Factorys
Offensive structures (nukes and BFG’s)

Upgrade the regenades fully, starting with the nanoshield (which you should take immediately). Then work on upgrading your basic land forces. I tend to build a lot of adaptors, so I go for the direct fire improvement, the nanoshield, and then the 10% upgrades. Building 2-4 research stations with the extra mass from reclaiming enemy units helps with the upgrading.

Do not underestimate the power of reclaiming mass with your ACU. Similarly, don’t forget to build defensive turrets with excess mass (after securing your base and building research stations).

You may have to personally supplement the land forces initially, but your air force should be able to handle it later. Your ACU is also very effective at recliaming enemy experimentals for mass to build more units. Airnomo’s are an excellent counter to your renegades. However, when you have 40-50 of them, you will lose about 1-2 per Airnomo that you choose to destroy exclusively with your gunships, so don’t be afraid to use your gunships to destroy them as well.

The renegades can do everything that land units can do for the purposes of this mission (destroying coils, commander assination, defence), except they are not effected by engineers, and most enemy units. Opposing gemini fighters may prove a slight problem, but they don’t do a great deal of damage if you have the nanoshield and a bunch of AA at your base.

It is wise to split your gunships into two groups, one to do the coils, one to defend.

The opposing commander goes down easily with ~40 gunships.

Honestly, while skirmishes are much different, I don’t see any reason not to focus on building gunships in the campaign (except for one, perhaps two missions).

Or if you had searching through text files and love playing the game, just do the mission again (do it on easy difficulty if you like) and do not capture any of the Fatboy factories. Might sound crazy, but trust me it’ll work as that how I did it.

Aircraft are the easiest way to attack his base as they can’t be countered by the Fatboys, and that sounds like what you’re doing.

Not sure I can I can offer any more help: Build lots of aircraft; do not capture his Fatboy factories.

Good luck!

Instead, build a ton of Bombers, Gunships, Mega Fortresses or what have you and directly assault the commander in his base. He will explode and that’s the end of the mission; no transports involved.

Don’t capture any of the experimental factories — you don’t need them, and they only increase your chances of failing the hidden objective.

Hope that helps!