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While awaiting reassignment following the destruction of the Enterprise, Worf took an extended leave of absence from Starfleet to evaluate his future. He returned his son to Earth to live with the Rozhenkos while he himself took refuge on Boreth.
(DS9: "The Way of the Warrior")

Captain Benjamin Sisko requested Worf's help as he was having trouble controlling the behaviour of Klingons when on Deep Space Nine.

Worf again became a player in galactic politics as the Federation tried to avert war between the Klingon Empire and the Cardassian Union. Worf felt the war was wrong and that it was incompatible with his loyalties with the Federation. Gowron threatened to strip Worf and his family of their honor, confiscate their lands, and treat them as traitors to the Klingon Empire.

The Klingons failed to bring down the Cardassian government with the Federation protecting them and an enraged Gowron withdrew the Khitomer Accords and made an enemy of the Federation. Worf considered resigning from Starfleet to take a berth on a Nyberrite Alliance cruiser. Learning of this, he offered Worf a position as the strategic operations officer, which Worf humbly accepted.
(DS9: "The Way of the Warrior")

Whenever Sisko was not commanding the USS Defiant, Worf got a chance to demonstrate his command expertise. One of the first missions he commanded was the science mission headed by Lenara Kahn.
(DS9: "Rejoined")

Whilst in the Gamma Quadrant, (the Defiant was escorting Quark to continue negotiations with the Karemma), the Jem'Hadar opened fire on them. Captain Sisko was severely injured in the incident, leaving Worf in command. Taking command in engineering Worf found many engineers were unaccustomed to his authoritarian style of command. After receiving advice from Chief O'Brien, Worf undertook a more interactive approach.
(DS9: "Starship Down")

In a subsequent mission, Worf commanded the Defiant on a mission to escort Cardassian freighters across a volatile sector of Klingon space. After being fired upon by Klingon warships using a tactic of continually decloaking to fire and then recloaking, a Klingon ship decloaked directly ahead of the Defiant and Worf ordered it destroyed. But this was a Klingon civilian transport ship. The Klingon Advocate Ch'Pok demanded that Worf be extradited to the Klingon Empire for punishment.

The Federation decided to stage an extradition hearing with Admiral T'Lara as chair and with Sisko as defense, and Ch'Pok as prosecution. Had it not been for Odo's discovery that there were no civilians on the destroyed ship, Worf would have been extradited to the Klingon Empire to face execution. (DS9: "Rules of Engagement")

Following a year of hostilities and border skirmishes between the Federation and Klingons Odo discovered that Gowron may have been replaced by a Changeling. In order to establish whether Gowron was a shapeshifter, Starfleet Command ordered Sisko to lead a team (which included Worf) to expose Gowron as a shapeshifter.The plan worked out relatively well on the surface, and Sisko was ready to activate the polaron emitter. However, just before he could activate the emitters, Martok, chief military adviser and overseer of the Cardassian invasion, recognized Sisko through his Klingon disguise, and the entire team were thrown into prison. While incarcerated, the team managed to explain their mission to Martok. It turned out that Martok had always suspected that Gowron may have been a Changeling, but he was waiting for the right time to expose him. Worf was then able to expose the changeling.
(DS9: "Broken Link", "Apocalypse Rising")