Uncle dies during the last mission, when the FBI storm the ranch at Beecher's Hope. Him and John see them coming from over the hill, they get Jack and Abigail to go the house. After a firefight, they get back to the house, Jack comes out to help, and Uncle gets shot on the front porch.
Edgar Ross takes Abigail and Jack, and uses that as leverage to get John to hunt and kill the last remaining members of his gang, so Bill, Javier and Dutch.
Dutch shows up towards the end, after Mexico/when you get back to Blackwater. He's only in a few missions, and he's unhinged. He takes and kills a hostage in Blackwater, and he is up in a camp north of Tall Trees, where he has a gang of Indians helping him. John goes after him, and chases him to a cliff, where Dutch talks about how the West is changing, before he walks off the edge. At the bottom, Ross uses John's gun to shoot him, saying it'll look better on the records the way, and tells him his family is back at the ranch.
Location wise, the entirety of America from RDR is in RDR2, it's just Mexico that isn't available. There are some differences though, like I don't think the camp Dutch has in Tall Trees is there for example, and Armadillo is different for example.