In early 2006 Brubaker wrote two limited series for Marvel; with artist Pablo Raimondi, he wrote Books of Doom, which retold and expanded on the origin of Doctor Doom; and with artist Trevor Hairsine, he wrote X-Men: Deadly Genesis, ret-conning information about the origins of the "All New, All-Different X-Men" who debuted in 1975.
He became the regular writer of Uncanny X-Men, working with artist Billy Tan and Clayton Henry, in July 2006. Brubaker, together with Matt Fraction, co-wrote a new Iron Fist ongoing series, The Immortal Iron Fist, which started in November 2006.