Last week I was driving my 2010 Ford Fusion Hybrid, and as I was rolling into a stop sign the brakes "went out," aka the hydraulic system failed and I had to stomp on the brakes for them to engage, bypassing the ABS system. It just takes a quick google search to see how many articles have been written about the issue.

I drove it to the Five Star Ford in Dallas, where they quoted me $2,100 for ABS Module replacement, HCU replacement, and brake flush. I haven't authorized them to start work yet.

I've done a lot of research over the last week and found that if my car would've been manufactured just a few months before, it would've been under Recall 19S54.
https://static.nhtsa.gov/odi/rcl/2019/RMISC-19V904-0442.pdf

There are hundreds if not thousands of complaints to NHTSA about the issue and Ford has not re-visited the issue.

Should I just authorize Ford service dept. to fix the issue according to what the recall says (brake flush and replace HCU) or fight it with Ford and try to get some sort of discount? Looks like a lot of people have tried to fight it and have come up empty handed.

First, I'm glad you werent hurt and were able to get the car safely stopped.

Second, unfortunately I don't think you're gonna get anywhere on a 10 year old car, are you the original owner, and have a good relationship with the dealer? They may goodwill a little bit if you have a service history there, but I dont think you're going to make any headway.

Third, there are many companies, Module Master, BBA, Upfix, MASRepair, etc that will rebuild yours for a fraction of the cost. The dealer has triple digit labor rates and won't 'think outside the box' and find a solution. They want to get it in and out and move on to the next repair. I've had some ABS modules for a texags customers Tahoe done at Module master. Mac Haik quoted them almost 3K to fix. I got him sorted for 25% of that.

Either DIY or find a decent honest mechanic and send yours off for a rebuild. $2100 bucks is about 60-70% of the value of a 10 year old FFH. You can get it done for less than half and use the money saved to Uber or Turo a rental car while they turn that module around.

From calling local mechanics that have Ford capabilities, they claim they can't do much cheaper. I think the only place they have wiggle room is on the labor. The breakdown of the Ford estimate is:
Labor (4.5 hr): $650
ABS Module: $856
HCU: $568
Brake fluid: $46

The biggest thing that concerns me is that Ford is saying they're going to replace the ABS Module first and if that doesn't work then they'll replace the HCU. They are taking the "shotgun approach." I think I've read every single forum on the topic in the past week and the general consensus is the problem is either fixed with a good brake flush with DOT 4 or replacing the HCU. Neither of those required replacing the ABS Module. I would hope this would be the case.

At this point I think I am leaning towards letting a local mechanic take the money for it (and maybe save a couple hundred bucks) and just start by a brake flush / HCU replacement.
I'd love to DIY it but I don't have the Ford IDS system which would be necessary for bleeding the new HCU.

Dont agree to the shotgun approach.

Thats ridiculous.

Found a local guy here who says he can do it, hes just swamped. Hopefully he'll give me another opinion and I wont have to sell this thing for parts.