On August 4, 2006, WWE announced that Hardy had re-signed with the company. In the following weeks, Jeff Hardy vignettes aired hyping his return on the August 21, 2006 episode of RAW. At his return he defeated Edge by disqualification. After failing to capture the Intercontinental Championship from Johnny Nitro over the next few weeks, including at Unforgiven 2006, Hardy finally defeated Nitro to win his second Intercontinental Championship on the October 2, 2006 edition of RAW. On the November 6, 2006 episode of RAW, Hardy lost the Intercontinental Championship back to Johnny Nitro, after Nitro hit him with the Intercontinental Championship title belt. Just a week after he lost the Intercontinental title to Nitro, Hardy regained it on the November 13, 2006 edition of RAW, with a crucifix pin. This marked Hardy's third reign as Intercontinental Champion.
On the November 21, 2006 episode of ECW on Sci Fi Jeff teamed with his brother Matt for the first time in almost five years. They had their old titantron video and music and defeated the Full Blooded Italians. At Survivor Series 2006, these two were in team DX against Team Rated-RKO, over whom they gained the victory with a sweep. Jeff and Matt then got their first opportunity since teaming up to win a tag team championship. They competed in a 4-team, for the WWE Tag-Team Championship in a Ladder match at Armageddon 2006, but came up short in their attempt.
With Jeff Hardy still feuding with Johnny Nitro and MNM into 2007, Jeff was challenged once again by Johnny Nitro at New Year's Revolution 2007 in a Steel Cage Match for the Intercontinental Championship, Hardy once again defeated Nitro. Then at the Royal Rumble the Hardys defeated MNM and at No Way Out 2007 The Hardys teamed with Chris Benoit to defeat MNM and Montel Vontavious Porter. The next night on RAW, Hardy was defeated for the Intercontinental title by Umaga.