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Death of Carl and band name litigation

Early in 1997, Carl was diagnosed with lung and brain cancer after years of heavy smoking. Despite his terminal condition, Carl continued to perform with the band on its 1997 summer tour (a double-bill with the band Chicago) while undergoing chemotherapy. During performances, he sat on a stool and needed oxygen after every song. Carl died on February 6, 1998, at the age of 51, two months after the death of the Wilsons' mother, Audree.

After Carl's death, Jardine left the touring line-up and began to perform regularly with his band "Beach Boys: Family & Friends" until he ran into legal issues for using the name without license. Meanwhile, Jardine sued Love, claiming that he had been excluded from their concerts, BRI, through its longtime attorney, Ed McPherson, sued Jardine in Federal Court. Jardine, in turn, counter-claimed against BRI for wrongful termination. Courts ruled in Love's favor, denying Jardine the use of the Beach Boys name in any fashion. However, Jardine proceeded to appeal this decision in addition to seeking $4 million in damages. The California Court of Appeal proceeded to rule that, "Love acted wrongfully in freezing Jardine out of touring under the Beach Boys name", allowing Jardine to continue with his lawsuit. The case ended up being settled outside of court with the terms not disclosed. BRI ultimately prevailed.

Jardine's final appearance with the band for more than a decade occurred on May 9, 1998, which was the final official Beach Boys show performed before the license dispute. During the license dispute, Love (with Marks) toured as "The California Beach Band"; it was previously believed he did so "America's Band", but this has since been disproven. Love then continued touring with Johnston (and David Marks, until he left the band again in 1999, due to health issues when he was diagnosed with hepatitis C), after securing a license from BRI, with the first performance of the 'reorganized' Love and Johnston-led touring band on July 4, 1998.

In 2000, ABC-TV premiered a two-part television miniseries, The Beach Boys: An American Family, that dramatized the Beach Boys' story. It was produced by Full House actor John Stamos, and was criticized by numerous parties, including Brian Wilson, for historical inaccuracies.

In 2004, Wilson recorded and released his solo album Brian Wilson Presents Smile, a reinterpretation of the unfinished Smile project. That September, Wilson issued a free CD through the Mail On Sunday that included Beach Boys songs he had recently rerecorded, five of which he co-authored with Love. The 10 track compilation had 2.6 million copies distributed and prompted Love to file a lawsuit in November 2005; he claimed the promotion hurt the sales of the original recordings and that his image was used for the CD. Wilson's wife Melinda alleged that, during the deposition, Love turned to Wilson and remarked, "you better start writing a real big hit because you're going to have to write me a real big check." Love's suit was dismissed in 2007 when a judge determined that there were no triable issues and that the case was without merit.

In 2006, Brian Wilson, Love, Jardine, Marks, and Johnston participated in a non-performing reunion on the rooftop of the Capitol Records building in Los Angeles to celebrate that the compilation album Sounds of Summer: The Very Best of The Beach Boys had been certified double-platinum. Later that year, Jardine joined Brian Wilson and his band for a short tour celebrating the 40th anniversary of Pet Sounds.

In 2008, Marks briefly reunited with Love and Johnston's touring band for a tour of Europe.

In 2010, Jardine released A Postcard from California, his solo debut, in June 2010 (re-released with two extra tracks on April 3, 2012). The album features contributions from Beach Boys Brian Wilson, Carl Wilson (posthumously), Bruce Johnston, David Marks, and Mike Love. Other guests with Beach Boys connections included Glen Campbell, Scott Mathews, Stephen Kalinich, and Gerry Beckley and Dewey Bunnell of America. Also in 2010, Brian Wilson and Jardine sang on "We Are the World 25: for Haiti", a new recording of "We Are the World" (with partially revised lyrics), which was released as a charity single to benefit the population of Haiti.

Jardine made his first appearance with the Beach Boys touring band in more than 10 years in 2011 at a tribute concert for Ronald Reagan 's 100th birthday; at this concert, he sang lead on "Help Me, Rhonda" and "Sloop John B". He made a handful of other appearances with Love and Johnston’s touring band in preparation for a reunion.