The Battle of Alcatraz was a battle between the X-Men and the Brotherhood of Mutants over the handling of the mutant Jimmy and the Leech Cure that was derived from his DNA. The US Military also participated, albeit briefly in the battle. The battle ended in a massacre, wtih several mutants being killed by the Phoenix. It was the last major battle between mutants and humans before the rise of the Sentinels.
Following the discovery that his son was a mutant, Warren Worthington II began development for a cure of the X-Gene, creating Worthington Labs and operating out of Alcatraz Island. Using the orphan mutant Jimmy, they eventually managed to produce what they called the "cure". Although the cure was not authorized by the government, they did approve of it's weaponization. This led to Hank McCoy resigning from his position in the government.
The cure also created friction between humans and mutants, with the latter believing the former being out to exterminate them. Hence, masses joined the Brotherhood of Mutants in an attempt to fight the cure, with Magneto wanting to kill Jimmy to stop the cure from being produced.
The battle commenced at Alcatraz, with the Brotherhood attacking the Worthington Labs facility. Many of the mutants were used as cannon fodder to waste the munitions of the US Army. Juggernaut was sent to try and kill Jimmy, but was stopped by Kitty Pryde. The entry of the X-Men in the battle saw Iceman triumph over Pyro and Wolverine, Colossus and Hank McCoy inject Magneto with the cure. After the Phoenix went berserk and began to massacre almost every mutant around her, the Wolverine, realizing his healing factor was the only thing stopping him from getting killed, went to confront her. Seeing she was hurting people, Wolverine reluctantly killed her.