starts off with Samus investigating a distress signal from a research vessel, a vessel that appears to have been overrun by Space Pirates, though most of them are already dead. At this point in the game, Samus has a few of her advanced abilities, but soon after her first Boss Battle, she is reduced to her basic suit and beam weapon.
Samus spends the remainder of the game trekking across Tallon IV, hunting baddies, both old and new, and rebuilding her arsenal. The arsenal within Prime contains all of her classic weapons, Plasma Beam, Wave Beam, etc, as well as a few new goodies.
One of her new attributes is the Grapple Beam, which enables Samus to swing across large gaps in the floor. Samus has also gained the ability to switch between her different beam weapons, whereas in the older games, she was only able to use the last obtained beam upgrade.
Another addition to the game is the need and use of different Visors. Each new Visor adds a level of complexity to the game, because by switching views, Samus gains the ability to see an enemy that she couldn't see before, or reveal passageways that are otherwise hidden. Along with the different views, the HUD system displays other needed information like Health, Maps, Weapons Data and Danger Assessment.
As an added bonus, if you hook up a Game Boy Advance to Metroid Prime with a completed game of Metroid Fusion, you are able to play through the original Metroid game.