Hardy debuted in Total Nonstop Action Wrestling on June 23, 2004 at the TNA Second Anniversary Show in a match against TNA X Division champion A.J. Styles, for the title. He also debuted his new entrance theme "Modest" and his nickname was The Charismatic Enigma. The match ended in a no-contest when Kid Kash and Dallas interfered. Hardy returned to TNA on July 21, 2004, and was awarded a shot at the NWA World Heavyweight Championship. Hardy challenged for the title on the final weekly TNA pay-per-view on September 8, 2004, losing to NWA World Heavyweight Champion Jeff Jarrett.
Hardy teamed with A.J. Styles and Ron Killings throughout mid-2004. In October 2004 he won a tournament, earning a shot at the NWA World Heavyweight Championship on November 7, 2004 at Victory Road 2004. Hardy was defeated by Jarrett once again in a ladder match at Victory Road following interference from Kevin Nash and Scott Hall. One month later on December 5, 2004 at Turning Point 2004, Hardy, Styles and Randy Savage defeated Jarrett, Hall and Nash (collectively known as the Kings of Wrestling). Hardy went on to defeat Hall in a single match at Final Resolution 2005 on January 16, 2005.
At Against All Odds 2005 on February 13, 2005, Hardy lost to Abyss in a "Full Metal Mayhem" match for the number one contendership to the NWA World Heavyweight Championship. However, he went on to defeat Abyss in a falls count anywhere match at Destination X 2005 on March 13, 2005. Hardy then went on to feud with Raven, with Hardy defeating Raven in a steel cage match at Lockdown 2005 on April 24, 2005. Hardy was suspended from TNA after no-showing his "Clockwork Orange House of Fun" rematch with Raven at Hard Justice 2005 on May 15, 2005, allegedly due to travel difficulties. Hardy's suspension was lifted on August 5, 2005, with Hardy returning to TNA at Sacrifice 2005 on August 14, 2005, attacking Jeff Jarrett. He wrestled his first TNA match in four months at Unbreakable on September 11, 2005, losing to Bobby Roode following interference from Jarrett.
Throughout October 2005, Hardy became embroiled in a feud with Abyss, Rhino and Sabu. The four way feud culminated in a Monster's Ball match at Bound for Glory 2005 on October 23, 2005, which was won by Rhino. In the course of the match, Hardy delivered a Swanton Bomb to Abyss from a height of approximately seventeen feet (5.18 meters). Later that night, Hardy competed in a ten-man battle royal for the number one contendership to the NWA World Heavyweight Championship, which was also won by Rhino. At Genesis 2005 on November 13, 2005, Hardy lost to Monty Brown in another number one contender match.
Hardy was scheduled to wrestle on the pre-show of Turning Point 2005 at December 11, 2005, but once again no-showed the event, again citing traveling problems. Hardy was suspended as a result and did not appear in TNA again. In March, April and May 2006, Hardy appeared on several house shows promoted by TNA in conjunction with Dave Hebner and the United Wrestling Federation.