In the alternate ending Kenshin never forgives himself for being a murderer. He's haunted by PTSD, his body is worn down from a life dedicated to fighting, and after the war ends he struggles to find a use for himself when the only thing he's ever known is how to swing a sword. So he wanders about Japan alone searching for a purpose leaving Kaoru and his son behind for months on end while she just sits there waiting for him to return sharing his pain.
Kenshin -
Kaoru -
totally unrecognizable from what we see of them in the anime.
Meanwhile Kenshin's friends notice he's dead inside and try to rescue him from depression.
that's his greatest rival realizing that Kenshin is a shell of himself and trying to help him in whatever way he can, as a friend. Doesn't work.
Lots of years pass and Kenshin gets an incurable disease that is contagious. Kaoru has dedicated her life to Kenshin, wants to die with him, contracts the disease and they both die in the end leaving their child behind.
A lot of people don't like the ending. But I think it's more realistic to the post war experiences of samurai and war veterans who don't get happy conclusions and spend the rest of their lives in misery.