Henderson returned to the light heavyweight division to face former UFC Middleweight champion Rich Franklin on January 17, 2009, at UFC 93 in Dublin, Ireland. Henderson won the fight via a split decision following an eye-poke in the third round that many, including Franklin, thought was intentional. He was subsequently selected to lead Team U.S. on season 9 of The Ultimate Fighter, with Michael Bisping coaching the opposing Team UK.
The reality TV show, which spawned a feud between the two coaches that continued until their fight, aired on Spike TV and premiered on April 1, 2009, with the live finale on June 20, 2009 in Las Vegas.
On July 11, 2009 at UFC 100 at the Mandalay Bay Events Center in Las Vegas, Henderson and Bisping fought, culminating in Henderson becoming the first man to knock Bisping out, doing so in the second round with an overhand right to the jaw as Bisping was circling to Henderson's right. This win put Henderson back into contention for a title shot at the UFC Middleweight Champion. The knockout punch won Henderson a $100,000 bonus for "Knockout of the Night" and is considered one of the greatest knockouts in the history of the sport.
Dan Henderson signed a four-fight, 16-month deal with Strikeforce on December 5, 2009, after his contract expired with the UFC. Henderson made his Strikeforce debut on April 17, 2010 at Strikeforce on CBS against Jake Shields. He was also eyed for a light heavyweight match against Gegard Mousasi, and expressed interest in eventually fighting Fedor Emelianenko at some point during his contract. Henderson lost his Strikeforce debut to Jake Shields. Despite hurting Shields and knocking him down in the 1st round, Henderson went on to lose by unanimous decision. The majority of the last rounds were spent on the ground where Shields controlled the fight via grappling. (49–46, 49–45, 48–45).