The Ultimates receive a new creative team with a very different approach by Jeph Loeb and Joe Madureira. This series marked a return of Joe Madureira to Marvel after a ten-year absence.
When the Scarlet Witch is murdered, the Ultimates find themselves in a war with the Brotherhood of Mutants, leading to massive casualties on both sides. This series was poorly received due to casual character deaths, a wildly different tone, and explicit acknowledgement of the incestual relationship of Quicksilver and Scarlet Witch (which was made implicit in the previous series).
This series led directly into the Ultimatum crossover event, also by Jeph Loeb.
Brotherhood of Mutants
The Ultimates 3: Who Killed Scarlet Witch
Ultimates 3 #1-5