He returned to DC in 2005, where he provided art for storylines such as Batman: Cacophony, "Whatever Happened to the Caped Crusader?, "Blackest Night", "Flashpoint", and The Dark Knight III: The Master Race.

[13] With writers Bill Jemas, Joe Quesada and Paul Jenkins, Kubert produced the Origin limited series which revealed the early history of Wolverine.

[14] Kubert collaborated with novelist Neil Gaiman on the Marvel 1602 eight-issue limited series published from November 2003 to June 2004.

[15] Writer Orson Scott Card and Kubert crafted the Ultimate Iron Man limited series in 2005.

[17][18] Andy Kubert became the penciller of the Batman series and with writer Grant Morrison introduced the Damian Wayne character.

[22] While his brother Adam has returned to Marvel Comics following his three-year deal with DC, Dan DiDio confirmed in 2009 that following "Whatever Happened to the Caped Crusader?

[27][28] In 2013 Kubert wrote and drew Damian: Son of the Batman, a four-issue mini series about Robin in an alternate future.

[29][30] Kubert was one of the artists on The Dark Knight III: The Master Race which was co-written by Frank Miller and Brian Azzarello.

[32][33] In 2020, DC Comics announced that Kubert would be among the creators of a revived Batman: Black and White anthology series to debut on December 8, 2020.