This part will break down a path through the planet ZDR, and is taken from NeoChozo's written guide on GameFAQS, with minor updates scattered throughout to account for technique updates. It will be broken down into smaller chapters designed to get you from one place to the next by tracking progress from one E.M.M.I. encounter to the next, with every bit of item acquisition encompassed within those segments. Directions are given assuming that the player knows where to go based on simple directions, i.e. "go left, then up, etc". The E.M.M.I. Zones are particularly detailed just because they can be maze-like in their layouts. On that note, the E.M.M.I. Zones are separated into their own sections within this walkthrough, but are only written as such until the E.M.M.I. in that area has been defeated, after which point they will be included as any normal room or area.
For item tracking and numbering, each main upgrade is listed in bold when you acquire it, but it is important to remember that the only things that count for percentage are the Missile Tanks, Energy Tanks, and Power Bomb Tanks that you pick up during the game. You will finish a 100% run with a grand total of 275 Missiles, 15 Power Bombs, and 12 Energy Tanks. If this sounds like a lot of stuff to collect, that's because it is. Like Mercury Steam's previous game, Metroid: Samus Returns, the typical pattern of "100 items to collect; 1 item is 1%, etc" is not adhered to. There are 123 Expansions in the game alone that account for your total item percentage, but if you are considering every item, upgrade, and pickup you have a total of 145 (147 counting the final end-game items that you lose anyway). This is why the item numbering through the walkthrough will not have percentages attached to them; at the end of the day, it is impossible to tabulate it accurately. All suit upgrades and other items will be listed like Charge Beam and Expansion-type items that count for percentage will be listed like Missile Tank (017/275). A slight exception is made for Energy Parts, however, even though there are a total of 16 in the game, it makes more sense to list them by how many you are carrying in order to create a full Energy Tank, such as Energy Part (2/4). When a 4th one is collected, the item total will update the number of Energy Tanks by 1.
As for the walkthrough itself, it is broken down into the aforementioned chapters below. Once you have beaten the game once, you can skip all cutscenes (except for the prologue) which can be a huge timesaver. Start a new file, watch the opening recap of Metroid Fusion's events and your arrival on the planet ZDR, then return to the menu as soon as you take control. Your save file should say 3 minutes and 44 seconds. This is what is considered a "starting" save file, and your timer begins here. For time calculation purposes in an actual speedrun, the 3:44 is subtracted from your final time. When the loading screen is over, you will begin in the depths of Artaria.