Numerous additions came in 1999 when the park was officially rebranded Six Flags Elitch Gardens. The first and most notable addition as a Six Flags theme park was Boomerang: Coast to Coaster. Various Warner Bros. properties, including the Looney Tunes and DC Comics franchises, were also introduced, which including costumed characters and shows.

Throughout 1999 to 2001, additions were rushed in, such as the new Looney Tunes Movietown area of the park, as well as water rides and flat rides.

In 2002, the park added Flying Coaster, a suspended steel flying roller coaster. It was a prototype model, and suffered from numerous operational glitches. It ceased operation in 2008, and was eventually sold to Luna Park in Coney Island in 2010, where it was installed in 2011 after being refurbished and updated by ride manufacturer Zamperla.

In 2004, the park installed the Half Pipe coaster, one of three operating in the United States.

In 2005, Six Flags removed Chance-Morgan Chaos flat rides for safety reasons. The same year, the park added a vertical water slide called Edge to its Island Kingdom water park.

Also in 2005, control of Six Flags was obtained by Washington Redskins owner Daniel Snyder, in a proxy fight following a shareholder revolt, which led to Kieran Burke being ousted as CEO. Snyder installed friend and former ESPN executive Mark Shapiro as the company’s new CEO.

The park faced a grim future in 2006 when Shapiro announced that the company would sell off six of its properties. Costumed workers and entertainment workers were laid off as a part of cost-cutting.