I figure they'd come with you on the train to the Mojave, then at some point just end up estranged. Maybe Jericho's lung issues got the better of him and he went to rest/find treatment with the Followers? RL-3's power cells died and he's just sitting idle in Vic's shack? Cross found the MW BoS and integrated there? I could easily see most of them drifting off in their own directions when the LW settles into a boring 9-5 as a courier, Dogmeat aside.
Dogmeat, IMO, should be placed somewhere in Doc Mitchell's. He's the one oddball that shouldn't be 'fired' per se, that'd stay with the LW throughout the 9 years of being a courier. Perhaps he ran off to fetch help when Benny captures you, thus revealing where you are to Victor? Maybe Benny shot him too and Doc patched him up in another room?
I'd also like to see Dogmeat and ED-E getting along. Rex is known to hate ED-E, but Dogmeat is entirely indifferent towards robots, so there's no reason for Dogmeat to object.
Patrollin' the Capitol Wasteland makes me wish for a nuclear winter...