Even Soujiro's great skills were unable to save him when the Bear, avatar of Hokkaido's Pattern, burst forth from the headquarters of the First Troop. The best thing that can be said about his end is that it was swift.
The poison-weakened Saitoh was beaten down by Bishou and Katsura near the end of the final battle, as the Ishin forces took control of Kyoto. He was imprisoned, then later recruited by the Ishin for the security forces of the new government.
After having worked with the kami Susanowo to summon the Guardian of Kyoto, Gojira, to battle the Bear, Anji chose to stay on as the High Priest under the new Ishin government.
Like Soujiro, Tomoe died when the Bear exploded out of the headquarters of the First Troop. Then again, she supposedly died once before...
Aoshi was killed by Bishou in the final battle. His giant chia pet saw a lot of use after his death, though.
Kenshin stayed in Kyoto while the other Ishin went off to kill people after the rising of the Bear. He probably did something like saving widows and orphans from rampaging xenofungus. Puss.
After being beat down and burned by Enishi, Shishio died when Shigeru's dying spikard-backed AKIRA!!! spell blasted him to ash. It was a pretty lousy day for him, all told.
Yumi died messily when her flying spell cut out during the assault by herself, the Presidents and Bishou upon the chia pet. The spikard she had acquired from Shigeru would have saved her if magic had been working--unfortunately, it wasn't.
Sanosuke's biggest accomplishment was to beat the Savage Jungle Drums, causing the sunken continent of Assyria to rise from the ocean and attack Kyoto. Bitch.
Megumi spent the final battle sitting in the middle of Kyoto's Pattern with Anji in case it was attacked. It wasn't, amazingly enough.