Here's the order of the Ultimate's adventures:
Ultimates: Super-Human
Ultimates: Homeland Security
Ultimate War
Ultimate Six
Ultimate Nightmare
Ultimate Secret
Ultimate Deathlock in USM
Ultimates 2: Gods and Monsters
Magnetic North
Ultimates 2: Grand Theft America
Ultimate Extinction
Ultimates 3
Why? Cuz, Obviously The whole Ultimates 1 has to happen first, and then with no interuptions for the Ultimates Ultimate war happens next. It has to because Black Widow and Hawkeye are public members at this point, and QS and SW are still shadow ops. Then Ultiamte Six occurs, QS and SW are still shadow and still no interuptions from other storys being written. Then Ultimate Nightmare occurs and Ultimate Secret. Ultimate Secret Occurs before Ultimates 2: Gods and Monsters because Thor is still up and going with the team, and Black Widow still doesn't have an assault suit. Same for engaging Ultimate Deathlock. Then Ultimates 2: GAM followed by Magnetic north because Black Widow has her assault suit, but still no traitor. Then Ultimates 2: GTA. Ultimate Extinction will be last because it will be written after Ultimates 2 is over and the writer will follow what he knows from Ultimates 2: GTA. The obviously Ultimates 3 will take place after that.