After the horrors of the impact crater, you'll wind up in a lengthy tunnel with Metroid Prime at the other end. The trick to this boss is to attack it with the beam that matches the colour of its armour: power beam for yellow, wave beam for purple, etc.
Target the face and use the appropriate beam for its armor. The super missiles and ice spreader weapons are excellent for dealing Prime some damage in it's yellow and white forms, respectively. During the battle, Metroid prime will fire beams, missiles and launch slower projectiles at you. Most of the projectiles can be destroyed for occasional refil items.
After enough damage has been dealt, it may charge to your side of the room. You can avoid this attack by switching to morph ball form and rolling down one of the grooves in the floor. Alternately, Prime may burrow it's way into a deeper chamber.
Continue this process throughout a total of four chambers, and when all of Metroid Prime's health is gone, it will drop down into the final chamber.
In its final form, Metroid Prime will hover around, causing shockwaves on the ground, swiping at you, and summoning pairs of metroids. Shockwaves can be jumped over easily, and metroids are best taken out with a single power bomb. Needless to say, you shouldn't be standing anywhere near the boss.
During the final battle, Metroid Prime will switch between visible spectrums, so you'll be constantly switching visors to keep track of it. Dodge the boss' attacks until it forms a pool of phazon (and creates some metroids.)
To defeat Metroid Prime, you'll need to step into these pools of phazon to activate Samus' hyper beam. The hyper beam will take off a decent portion of Prime's health, and will force it to switch to a new spectrum.
It will take about eight full blasts from the hyper beam to defeat Metroid Prime and end its reign on Tallon IV.