The organisation plays a large part in Marvel's "Dark Reign" and Siege storylines that ran from 2008 to 2010.

[1] Also, in the Captain America: Reborn Prelude, when Sin, who is captured by H.A.M.M.E.R, asks what it stands for, the agent present claims that it's classified information which she does not have the necessary security clearance to divulge.

The ramifications of the alien Skrulls' invasion of Earth forced a massive restructuring of the United States' defense network.

At the time, the country's primary peace keeping agency was S.H.I.E.L.D., led by civilian industrialist Tony Stark, aka, Iron Man.

In the wake of this controversy, Thunderbolts leader Norman Osborn manipulated the U.S. government into allowing him to serve as director of a replacement agency called H.A.M.M.E.R.

's image more palatable to the general public, Osborn reorganized the Avengers, filling their ranks with members of the Thunderbolts.

[6] The President was watching the invasion of Asgard with his security council; he ordered the Secretary of State to dispatch all available military forces to Broxton and to have Osborn and the Dark Avengers arrested for treason.

The President then decided to let Captain America deal with Osborn and sent an order to the arriving military forces to focus on H.A.M.M.E.R.

[8] Some remnants of the organization attempted to reorganize themselves after Osborn's defeat, contacting Victoria Hand to lead them, only to have her give their location to the New Avengers in her new role as their S.H.I.E.L.D.

Orchis began building cosmic-level Sentinels in an orbital base to take on mutantkind after Professor X turned Krakoa into a sovereign nation state for mutants and used its unique abilities to created massive plantlike "Habitats" with embassies around the world.

Through the combination of technology and mutant power, Professor Xavier developed three drugs that could change human life: A pill that extends human life by five years, an adaptable universal antibiotic, and a pill that cures “diseases of the mind, in humans.” In exchange for recognizing the sovereignty of Krakoa, Professor X said he will give these drugs to mankind, with mutants living in peace on the island.