This ended the first epoch of the Great Galactic War. There would be peace for the next thirty-five years. During this time, 5010 tried numerous times to become a member of Science Team, believing his mind would be of great assistance to the Armada. Time and time again he was turned down. After his fifth try, he took his case up with High Command. They denied his request, but the current Supreme Commander, Argross, noticed potential in 5010. Argross had become Supreme Commander shortly before the first epoch ended. His promotion left a vacancy in the High Command, and Argross decided to fill it with 5010. At his coronation ceremony, 5010 cast away his number, and became known only as "Commando 005" from that moment on. During the years that followed, Argross rebuilt the Armada's military, believing the second epoch to be coming shortly. Though he was right, he never lived to see the second epoch's coming; Commando 005 killed him, and took his place as Supreme Commander. Forty years had passed since he had made the deal with his brothers. As per the deal, he reorganized the security forces, placing them under the control of 1210, and making 3910 the 2nd in command.

To fill the several vacancies of High Command, he selected 4765, who then became "Commando 006", as well as former Imperial Marshal 3447, who became "Commando 004". To fill the place of Imperial Marshall, he selected General Ridley, who had served admirably during the first epoch. Commando 005's 2nd in command was decided as Commando 001, former Senior Marshall of the Air Force, and highest decorated soldier of the first epoch. Deciding that all was as he wanted it, Commando 005 sent several armored divisions into occupied Federation territory, starting the second epoch.

During the early years of the second epoch, Commando 005 sought to create alliances with other races, to help in the war effort. He successfully recruited the KiHunters, who would become his personal bodyguards and assassins. Their speed and steadfast determination also made them very successful frontline troops. His ability to anticipate the movement of Federation troops, and quickly blitzkrieg them with armored divisions would gave him victory after victory. But their resources ran ever lower. Deciding that the only way to win the war was to seek out new energy, he sent exploratory teams to other planets. This was how the Pirates first made contact with the Chozo. This was also how the Pirates would create their greatest adversary.

It was early 2048 C. C. An exploratory team had discovered a highly concentrated energy source-Afloraltite. It was being mined on Federation colony K-2L. Ridley personally oversaw the operation. He also participated in the slaughtering of every man, woman, and child on the colony, save for one-Samus Aran. In the later years of the war, she would become the greatest adversary the Armada would ever know. She spoiled every plan the Pirates made, from their Zebes operations, to Operation Seelöwe, the invasion of Norion. She had made it her mission in life to eradicate their existence from the galaxy. After the events onboard the B. S. L. labs, the Federation labeled her a criminal, and, with their greatest treat out of the way, the Armada was able to counterattack with a vengeance. But soon, the Federation realized they needed Samus, and struck a deal with her-All criminal charges would be dropped, and she would be placed as Supreme Commander of all future Federation military activity, until the end of the war. With her in command, the Federation was able to advance rapidly, crushing the Armada.