In short, Ryoma's ideas were just too modern for the others to accept or understand. Many, including the Shishis, began to fear his existance, though he declined to take part in the new government at all. This was perhaps the cause for his assassination on November 15, 1867, in which his friend cum colleague, Nakaoka Shintarou died with him. His assassins were never traced down. Ryoma died during the night of the assassination, but Nakaoka only died after three days. During those three days, he told of how Ryoma tried to get help for him by crying out, not realising that he himself was suffering from a much more serious wound. Then Ryoma felt the blood trickling from his split skull onto his hand, and knew that his end was near, and said such to Nakaoka with his dying breath.
The editors of Kenshin Hiden hazarded a guess that Kenshin may have been the hitokiri involoved (provided Himura Kenshin existed at all, of course) but I feel that it's NOT Kenshin's work. Because by the time Ryoma was killed, Kenshin was no longer working as an assassin, but the protector of Ishin Shishis and a warrior in the Boshin war, as Sanosuke tells us before his first match with Kenshin.
The following year, 1868, after Yoshinobu escaped to Edo when Satsuma and Choshu won the Boshin War and sent armies after him, Katsu Kaishuu negotiated with Saigo Takamori, and Edo surrendered without any bleeding. The new era of Meiji had begun.