By the mid 24th century, the clerics saw that the Klingon ideals expressed by the original Kahless had become corrupted, and that the Klingon people had lost their way. Feeling that the people needed a spiritual figure to rally behind, they decided to take genetic material from the original Kahless and create a clone. They programmed the clone with the memories of the original Kahless - including the story of the original bat'leth, which was known only to certain clerics.
The deception was soon exposed when Chancellor Gowron defeated Kahless in combat. Worf felt that the Klingon people still needed a symbol, and proposed that the clone become the ceremonial Emperor of the Klingon Empire, the first in 300 years, while the actual power would still rest in the Chancellor and the High Council. (TNG episode: "Rightful Heir")
Worf intended to give the Sword of Kahless to the Emperor to unify the Great Houses against Gowron, although Kor thought Kahless was a pretender and a toothless figurehead. (DS9 episode: "The Sword of Kahless")
In late 2375, Kahless aided Martok, Worf and Alexander Rozhenko when Morjod and Gothmara attempted to usurp the throne from Chancellor Martok. (DS9 - The Left Hand of Destiny novels: Book One, Book Two)
In 2379, the Klingon rebel group Klahb took over the Federation Embassy on Qo'noS and demanded, among other things, that the hologram posing as Kahless be deactivated. Until then, Martok and the High Council had been unaware of the duplicity. Many believed that the Federation was responsible for kidnapping Kahless and replacing him. This belief was further fueled by the discovery that the hologram was kept active by a copy of the mobile emitter that the USS Voyager brought back from the Delta Quadrant.
As it turned out, Kahless had replaced himself to see "how long it would take you to notice." The answer turned out to be six months. After getting help from discreet Klingon friends, Kahless traveled to Cygnet IV where he took up painting. He was found by the USS Enterprise-E and taken back to Qo'noS where he told Martok that he was no longer needed. After undergoing the vIt 'Iw tay ritual, he returned to Cygnet IV to allow himself time to be selfish and to do whatever he wanted. (TNG - A Time to... novel: A Time for War, A Time for Peace)
In 2403 Kahless departed Qo'noS for parts unknown, handpicking a crew from the Order of the Bat'leth for his flagship IKS Batlh. He left a message behind saying that the Klingons no longer needed his guidance and he would return when he was most needed. (STO website: The Path to 2409)
In 2409, following the Fek'Ihri attack on Qo'noS, a Klingon Defense Force vessel responded to a distress signal from the Batlh, which had come under Breen attack. The emperor had apparently been searching for the Sword of Kahless, and led the captain to the Boreth monastery so they could travel into Gre'thor to challenge Fek'Ihr and Molor. After the captain was successful, the clone gifted them a replica of the Sword of Kahless. (STO missions: "Destiny", "Afterlife", "The Gates of Gre'thor")
The following year, with the beginning of the Iconian War, Kahless was revealed to be the head of House Pegh, an elite group of warriors working clandestinely against threats of the Empire. Wielding the Sword of Kahless, the Emperor led a strike team - aided by Federation, Klingon, and Romulan Republic forces - to an Iconian facility dealing in the production of Omega molecules in the Dinasia system. On the surface of Dinasia Prime, he broke away from the main group and the mission plan to challenge the Iconian known as T'ket to single combat, while the strike force attempted to disable the Omega generators. B'Eler discovered that a weakness in the Iconians involving Omega, and temporarily disabled T'ket. Instead of striking the death-blow, Kahless told the Iconian he was victorious because he had honor on his side, at which point T'ket teleported behind him and ran him through. Upon seeing this, Ramir panicked, alerting T'ket to the team's position, and the strike force was forced to flee the planet with only one of three mission objectives successful (STO - "The Iconian War" mission: "House Pegh")