User blog comment:TheMG/New Metroid Answers Wiki/@comment-25546749-20100525204947

If you pause the game before the Omega Pirate is killed (which is before you get the Phazon Suit), you won't have the beam. If you check it again after you kill the pirate and get the suit, you will have the Phazon Beam. The official website even says that you get it when your suit is corrupted.

"The official website states: 'When Samus' Power Suit is corrupted by viral contamination, the Arm Cannon becomes capable of firing the powerful Phazon Beam.'" Taken from the Phazon Beam page.