In the years between 2000 and 2012, the JLA continues much in the same vein it does now-- roster occasionally changing, a member dying, retiring, marrying etc. throughout the years. Everything is pretty much status quo.
In 2006 Mister Miracle returns to New Genesis for good, to help keep tabs on Danger Girl's activities on Apokolips.
In 2008 Superwoman and Karate Kid resign, as they move on to form New Krypton. Superman first joins the League at this time, as her replacement. Val stays on with the Academy as an instructor. The League maintains close ties wit New Krypton in the following years. Disgusted with the increasing number of anti-Martian movies being produced by Hollywood, Martian Manhunter disappears.
In 2012, the Dominators make another attempt at Invasion, utilizing a cadre of Kryptonian clones they'd developed from Kal-El's DNA. The hybrids of China rise up to assist the world's heroes in driving off the invasion forces. Public sentiment towards the world's heroes is at an all-time high, while too much inner-strife amongst the League, and other teams, leads the League to disband.
In 2016 the League re-forms, led by Batman. The roster includes Aleea Strange, Archer, Superman, Kyle Rayner, Aquaman, Ink, Flash IV and Bullseye. While an occasional member would come and go, this team remains the core.
The League disbands in 2019 for varied reasons. Batman has too many conflicting interests pulling him in other directions. Flash's personal life is starting to grow strained by his having too many responsibilities. Bullseye turns out to be a hitman named Cadaver, killing Aquaman, and almost killing Ink, and escaping capture. The League then crumbles.
In 2020, Superman establishes the League's newest incarnation. Turned down by both Kyle and Bart, their numbers are replaced by Superman's wife Roxanne, and Haley Grayson. Old friend and some-time team-mate Lagoon Man comes on board to fill Aquaman's enormous shoes. They pull in various graduates of the Knight Academy to fill their roster.