Cash has an ability to cover a song and own it even more than the person who wrote it, "Hurt" being perhaps the best example. That wasn't who he was originally. He was a rockabilly/country, and then gospel/mainstream mix, carving out his own niche. That ability to interpret a song on the basis of everyone knowing who he was and what he had been through came much later.
So. He does this song well, even without Fiona Apple. But when she enters at about the two minute mark I go into tears every time. Not only is her harmony and phrasing riveting because it is unusual, but her beautiful and haunting voice is a lot like June Carter Cash. June was already dying when this was recorded, and Johnny would be dead in about a year as well.
Fiona does not simply provide her own depth with the sound, she magnifies his. Like a bridge over troubled water.