During the Australian leg of the HIStory World Tour, Jackson married dermatology nurse Deborah Jeanne Rowe on November 14, 1996 in an impromptu ceremony close to his Sydney hotel room. She gave birth to Michael's first two children: a son named Michael Joseph Jr (commonly known as Prince), and a daughter, Paris-Michael Katherine.Rowe and Jackson first met in the mid-1980s, when Jackson was allegedly diagnosed with vitiligo. She spent many years treating his illness as well as providing emotional support. They built a strong friendship, then became romantically involved.Originally, there were no plans to marry, but following Rowe's first pregnancy, Jackson's mother intervened and persuaded them to do so.The couple divorced in 1999 but remained friends, and Rowe gave full custody of the children to Jackson.

In 1997, Jackson released Blood on the Dance Floor: HIStory in the Mix, which contained remixes of hit singles from HIStory and five new songs. Worldwide sales stand at 6 million copies as of 2007, making it the best selling remix album ever released. It reached number one in the UK, as did the title track.In the US, the album was certified platinum, but only reached number 24.Forbes placed his annual income at $35 million in 1996 and $20 million in 1997.

Throughout June 1999, Jackson was involved in a number of charitable events. He joined Luciano Pavarotti for a benefit concert in Modena, Italy. The show was in support of the non-profit organization War Child, and raised a million dollars for the refugees of Kosovo, as well as additional funds for the children of Guatemala.Later that month, Jackson organized a set of "Michael Jackson & Friends" benefit concerts in Germany and Korea. Other artists involved included Slash, The Scorpions, Boyz II Men, Luther Vandross, Mariah Carey, A. R. Rahman, Prabhu Deva Sundaram, Shobana Chandrakumar, Andrea Bocelli and Luciano Pavarotti. The proceeds went to the "Nelson Mandela Children's Fund", the Red Cross and UNESCO.
2000–03: Label dispute, Invincible and third child

In October 2001, Jackson released Invincible. This was his first album in six years, and it turned out to be the last album of new material he released while still alive. The release of the album was preceded by a dispute between Jackson and his record label, Sony Music Entertainment.

Jackson had expected the licenses to the masters of his albums to revert to him sometime in the early 2000s. Once he had the licenses, he would be able to promote the material however he pleased and he would also be able to keep all the profits. However, due to various clauses in the contract, the revert date turned out to be many years away. Jackson discovered that the attorney who represented him in the deal was also representing Sony, creating a conflict of interest.Jackson was also concerned about another conflict of interest. For a number of years, Sony had been pushing to buy all of Jackson's share in their music catalog venture. Jackson feared that Sony might ironically have something to gain from Jackson's career failing, since if his career did fail he would have to sell his share of the catalog.

These conflicts were utilized by the entertainer to leverage an early exit to his contract.Just before the release of Invincible, Jackson informed the head of Sony Music Entertainment, Tommy Mottola, that he was leaving Sony.[106] As a result, all singles releases, video shootings and promotions concerning the Invincible album were canceled.

In spite of the uproar preceding its release, Invincible came out in October 2001 to much anticipation. Just before the album's release, a special 30th Anniversary celebration at Madison Square Garden occurred in September 2001 to mark the singer's 30th year as a solo artist. Jackson appeared onstage alongside his brothers for the first time since 1984.The show also featured performances by Mýa, Usher, Whitney Houston, 'N Sync, Destiny's Child, Monica, Luther Vandross, and Slash, among other artists.In the wake of the September 11, 2001 attacks, Jackson helped organize the United We Stand: What More Can I Give benefit concert at RFK Stadium in Washington, D.C. The concert was aired on October 21, 2001, and included performances from dozens of major artists, including Jackson, who performed his song "What More Can I Give" as the finale.

Invincible proved to be a hit, debuting atop the charts in 13 countries and going on to sell approximately 13 million copies worldwide. It received double-platinum certification in the US.However, the sales for Invincible were lower than those of his previous releases, due in part to a lack of promotion, no supporting world tour and the label dispute. The album also came out at a bad time for the music industry in general.[109] The album cost $30 million to record, not including promotional expenditures.
Invincible spawned three singles, "You Rock My World", "Cry" and "Butterflies", the latter without a music video.

Jackson alleged in July 2002 that Mottola was a "devil" and a "racist" who did not support his African-American artists, using them merely for his own personal gain.[109] He charged that Mottola had called his colleague Irv Gotti a "fat nigger".[114] Sony refused to renew Jackson's contract, and claimed that a $25 million promotional campaign had failed because Jackson refused to tour in the United States.
Jackson's third child, Prince Michael Jackson II (nicknamed "Blanket") was born in 2002.The mother's identity is unknown, but Jackson has said the child was the result of artificial insemination from a surrogate mother and his own sperm cells.[104] In November of that year, Jackson brought his newborn son onto the balcony of his room at the Hotel Adlon in Berlin, as fans stood below, holding him in his right arm, with a cloth loosely draped over the baby's face. The baby was briefly extended over a railing, four stories above ground level, causing widespread criticism in the media. Jackson later apologized for the incident, calling it "a terrible mistake".Sony released a compilation of Jackson's hits on CD and DVD. In the US, the album was certified platinum by the RIAA; in the UK it was certified for shipments of at least 1.2 million units.