This walkthrough for Metroid Prime 2 is split up in a logical progression to achieve a 100% completion in a reasonable amount of time and with manageable difficulty. For the most part the equipment upgrades must be collected in a certain order, so the game is fairly linear in that sense. There are, however, many secondary items (Energy Tanks and Missile Expansions, etc.) that are optional, though there are several bosses that will be difficult to defeat if you don't take the time to collect them when you can.
In addition to collecting all the items to be found, this guide will cover the log book entries that can be collected in the game. These are optional, but bonus materials become available when collection milestones are achieved. Many of these entries are "Missable", meaning they can no longer be collected after you reach a certain point in the game. In some cases the window of opportunity is very short, for example a single boss battle. This guide will warn you in these cases so you can be sure to collect the entries before it's too late.
Each article is named after a major area to be explored or item that must be acquired. Back tracking through areas is common.
Setting and backstory
Most of the game takes place on the planet Aether, home of the Luminoth civilization. Having reached a level of development comparable to the Chozo, the Luminoth settled on Aether to enjoy lives free from the cares of galactic exploration. As with the Chozo, an interstellar object collided with their new home, in this case causing a rift which split the planet into Light Aether and Dark Aether. These are parallel versions of the same planet, but very different. Soon the Luminoth came into contact with the Ing, the warlike inhabitants of Dark Aether who were intent on conquering or destroying Light Aether.
Meanwhile, the Space Pirates, having suffered a loss at the hands of Samus on Tallon IV, have discovered that Dark Aether is a rich source of Phazon. Fortunately, though the Pirates have established a presence on Aether, they have not formed and alliance with the Ing and the two races are as hostile to each other as they are to you. To futher complicate matters, some life force has merged with Samus' Phazon suit left behind on Tallon IV, creating the Dark Hunter. This Dark Hunter resembles Samus, but is actually her evil twin. She feeds on Phazon and is hostile to Samus when they meet.
Aether is divided into Light and Dark sides, and each side is divided into four areas. for a total of eight, each with its own character. Each area is subdivided into many rooms which show up as separate units on maps. The atmosphere on Dark side is poisonous, so you will constantly lose health there except in special protected zones. Fortunately you regain health while in these zones.