This is my second playthrough - on Xbox 360. I had Fawkes as my only companion the first time (and Dogmeat).

Now I had RL-3 and Dogmeat. You are, of course, separated from them when you go to Raven Rock.
After I escaped, I went to Vault 101 and picked up Dogmeat, then to Canterbury Commons for RL-3, who wouldn't follow me as my karma was now Very Good (which was annoying).

So I went to Megaton with Dogmeat and sneaked into a few places to steal enough stuff to lower my karma to neutral - it took a while! I was spotted in the Brass Lantern, but used a stealth boy which seemed to confuse them, and nobody attacked. When I went to leave all the stolen items were retrieved, which was okay as I didn't want them anyway!

Once my karma had dropped to neutral, I went to the main entrance, where Deputy Weld was being attacked by Yao Guai. I had Animal Friend level one, so they didn't attack me but they 'killed' Deputy Weld.

Anyway, Dogmeat was growling like mad, although there were no red dots on the compass. So I fast travelled to Canterbury Commons, and he was still growling. I approached RL-3 and he raced up to me, spouting a selection of the remarks he usually makes to enemies - but he didn't attack. There were no dialogue options.

I dismissed Dogmeat and fast travelled to the Citadel. The BOS troops outside, and the robot, started shouting about hostiles, and they all rushed up to me, but didn't attack. They followed me around until I left the area.

So after reducing my karma from Very Good to neutral by stealing, Dogmeat acts hostile when I leave Megaton, and I can't even talk to RL-3 (but I can talk to Dogmeat as normal).
(I tried recruiting Fawkes, but he wouldn't come with me as I was no longer good.)

I've had a quick search here, but can't see this issue mentioned. As I find RL-3 amusing to have around, I've reverted to a save before going to Vault 87.

I just wondered if anybody had any suggestions/observations.

Thanks

What was the time frame, for all these events to occur? Including all your fast travel and what not? If you turn people hostile towards you, they will be hostile for three days plus an hour. After this time, you'll be cool with everyone.
I've had companions turn on me, usually happens during a firefight when they cross in front of me and I shoot them by accident. One shot won't do it, but several will.... and as I use Eugene in non-VATS mode, I might accidentally concentrate some fire on them. Never, ever get Dogmeat mad at you.... he kills me every time.

Perhaps load the save after RR, make Dogmeat wait for you somewhere, as he will be hostile towards anyone who is hostile to you. Go lower your karma, escape town, wait for three days in Super Duper Mart or something, go back to Megaton, get Dogmeat and then go get RL3?

Thank you for your suggestions.

I read somewhere that if you kill a certain person in Underworld, if you return after 3 days the rest of them will no longer be hostile.

I'll try waiting for a few days to see what happens - and try hard not to let anybody see me in the first place!

I'll report how I get on.