I had a very similar problem a little over three years ago, when I introduced my resident kitty, Muffs (then only 5 mths) to my new kitten, Abby (10 wks). Muffs was terrified of Abby, although there was no hissing. Instead, Muffs would run and hide, unless she felt really threatened, whereupon she would turn on Abby and a fight would ensue. After a long slow introduction that had taken at least a month, we were getting nowhere. Long story short, I hired an animal behaviorist. I don't profess to be an expert. I can only tell you what I was told to do. I don't know whether it will or won't work in your case. Fortunately, it worked in my case. I have also outlined these steps for other members here in the past, and it has worked in their case too…so here’s hoping it works for you too.
First, keep them separated as you are doing. However, there needs to be some sort of “meeting place”, where the cats can come together, yet be separated by some sort of porous barrier. They need to be able to see and smell each other, but unable to physically interact. Some people have installed stacked baby gates in a doorway, with the cats on either side (in your case, two cats on one side and Cat #3 on the other). I kept Abby in my dining room (which has two entrances), and I temporarily affixed screens over one of the entranceways. A screen door would also work…basically whatever you have or can come up with temporarily. We will call this the area the “barrier”.
Put all food, water, and comfort objects (toys, etc.) within 2 ft of the barrier on either side (or as close as possible otherwise). Have all “good things” in life happen within 2 ft of the barrier in each other’s company (all attention, all feedings, all treats, any catnip, all playtime, any cat grass, any grooming, etc.). To the extent possible, NO good things are to happen anywhere else. If they want to eat they must do so at the barrier; all play happens by the barrier; all petting happens by the barrier; etc. Have at least 10 “events” (good things) happen each day. The fact that they only ever experience the good things in life when they’re together, and not otherwise, eventually conditions the cats to associate good things with each other and gives them a reason to like each other.
In addition, switch the cats for one hour each evening. During this time, just let them wander around freely in each other’s area…so, put Cats #1 and #2 in the area normally occupied by Cat #3, and put Cat #3 in the area normally occupied by Cats #1 and #2 (don’t let them meet or interact when you switch them). They need not be by the barrier during this hour. By wandering about during this hour, they will each start to get more accustomed to each other’s scents in a non-threatening way. Plus, they will be depositing their scent in the living area of the other, slowly creating a family or “communal” scent, which makes them feel like they all belong.
This entire process (good things by the barrier plus the daily room exchange) may go on for weeks. During this time, monitor their behavior. Once you start to see a reduction in reactivity – the cats no longer hissing, growling or acting frightened, starting to interact through the gate (playing footsies, etc.), then conduct a supervised 10-minute play session each day with the three of them together in an open area. After the session, separate them again and continue with "good things happening by the barrier". Over time, gradually increase the length or number of the supervised play sessions where they're all together.
I was quite skeptical that any of this would work, but after a week I started to see some improvement. After a few more weeks, Muffs and Abby began to play footsies under the screen and they started to touch noses through the screen. I then started to allow them out together for short, supervised play sessions. It took another 3 weeks or so before they could be out together all day (with me still home to keep a general eye on them). It took another month before I left them alone together when I was at work. Despite their horrible initial start, over the past three years, they have been best friends; they cuddle and groom each other, and you rarely see one without the other. They play-fight from time to time, but real fights never happen.
After he saw Muffs and Abby together at first, the behaviorist warned me that there was only a 50-50 chance of success (Muffs is an extremely timid cat and the behaviorist thought she might be better off in a single-cat home). So, mine was a success story and/or I got lucky. I will also note that this can be (and was) a lot of work. I spent hours by the darn barrier trying to get these two little ones to like each other, but it was worth it in the end. As I said above, I don't know if this will work for you. But, whether you try this or something else, I hope you have the same good luck!
P.S. I also used Feliway, which tends to help some cats, but not others. I found it helped Muffs, but had no impact on Abby. But it’s still worth a shot.