Johnny, assisted by Flash Perkins, finds the plantation home where his son is being cared for by the slaves (DeForest Kelley makes an appearance as a Southern officer who is wounded and captured by the pair). Susanna, however, is not there, she has essentially had herself committed after a nervous breakdown. Once they leave the plantation, though, they fall into an ambush. Flash, wounded, distracts the rebel soldiers and, sacrificing himself, buys Johnny enough time to escape with his son.
Eventually Johnny locates Susanna in a mental hospital and after much persistence convinces her to return with him to Raintree County. As the war winds down Johnny and Susanna try to return to a normal life, but her fragility is a constant source of heartache. Pressures within family and within County society begin to mount for Johnny to go into politics, but he resists.
Eventually, even though the family does their best to make her welcome, Susanna comes to the same conclusion as so many others – that Johnny is destined to be a Great Man, but that she herself has been the one thing preventing him from living up to his promise. Taking their son in her arms one night, she flees into the swamp. A search party eventually discovers her lifeless body (drowned, one is left to presume), and a despondent Johnny continues searching for his son. As the two are reunited, the camera pulls away, and we see that the tree under which the boy had been lying in the swamp was the long-lost raintree, though the characters themselves never see it.
Many apologies if this summary is inaccurate, misleading, incomplete, etc. I only saw the film myself for the first time a few weeks ago.