The Galactic Federation has called on Samus to locate Trooper Squad Bravo who lost contact 8 days ago while patrolling space around the rogue planet Aether. But Samus' Gunship is heavily damaged while heading through an atmospheric storm en route to the planet's surface and crash lands inside a building.
You start in Temple Grounds, which serves as the game's hub world. The first part is a training area, or really a warm up area since it's likely you've played the previous game in the series. You proceed along a relatively linear course, but there are some surprises on the way.
You take control of Samus on top of her Gunship, which you should scan right away for a Logbook entry. Stepping into the blue circle on top of the ship will allow you to save your game, as well as restoring all of your health and ammunition, which will come into play later in the game. Right now, however, your only weapons are the Power Beam, an unlimited-ammunition weapon that trades strength for a high rate of fire, the Charge Beam, a more powerful weapon which takes time to charge, and Missiles, high-explosive weapons that run on an ammo system. At the moment, you can carry 5 of these maximum. There's a purple crystal to the left of the ship, but you can't interact with it yet.
After you get used to the interface, locate the webbing blocking the passage in front of the ship. To get through, lock on to and blast the green orbs in the center with your Power Beam, then shoot the door to proceed.
Hive Access Tunnel
There is a fork in the passage, but the left path leads to a wall with the Violet hologram which can't be opened. So head right where you will jump down into a hole.
Hive Chamber A
The room is filled with a green gas, namely a type of industrial-grade pesticide, which explains the large pile of dead insectoid creatures around the room. The crates here are Federation supply crates which you can destroy to refresh your supplies. Get a scan of the gate for the Log, then scan the control panel, the small box with a rotating hologram displayed on it. These are used to activate machinery throughout the game, so make sure to scan them whenever possible. After scanning the module, blast the two red circles that appear above the gate to proceed.
In the next hallway, you'll have to turn to your right to scan another control panel to cause the cargo pod gate to recede. Scan the computer displays in the next section to learn about what's been happening here. The troopers had a makeshift base here and fought the native life forms called "Splinters". Step into the Map Station to download a partial map of the area. Destroy the webbing in the same manner as before to proceed to the next room.
This is a small passage with Worker Splinters, the first "enemies" in the game. They're harmless and power beam shots will quickly clear them. What's more worrisome is that they are feeding on what's left of the troopers, now just corpses dangling from the ceiling.
Scan the corpses on either side of the room for Logbook entries. There is a control panel next to one of them, but its power supply is off. Switch to Morph Ball to get under the large gate, head into the tunnel on the right, and use a bomb to clear the gate part way through. In the small room at the end, scan the Bomb Slot for the Logbook and activate it. (Drop a bomb and let it explode to propel you into the slot, then drop another bomb to activate the slot.) This restores power to the control panel in the first section, but it will also awaken several Dark Troopers, the game's first true enemies. They are actually the reanimated corpses of the troopers you just passed. Fortunately, whatever are controlling them aren't good shoots, but when they do hit they can do decent damage. Use the Charge Beam to take them down so you'll draw in the pickups they leave behind. Head back to the main room to fight more of the Dark Troopers, then scan the control panel. This opens the gate but releases yet more Dark Troopers.
There's not much of interest in this room. If you took a beating against the Troopers, blow the crates to get energy and ammunition restore power-ups. If not, just jump over the ones blocking the way.
Hive Chamber B
When you enter this room, you'll notice a mysterious figure entering an interdimensional rift. Follow the figure through and you'll watch a cinema showing it absorbing some phazon, and then a horde of creatures stealing Samus' items. Afterwards, you'll be left with your basic Varia Suit, Power Beam, Charge beam, Morph Ball, Combat Visor, and Scan Visor. (In the first game your Charge beam and Morph Ball were taken as well as you escaped the frigate, so consider yourself lucky this time.)
A quick note for later in the game: The portal here will NOT reappear; it can only be used once.
You won't be much use until you get your equipment back, so you now must begin the long, slow process of getting it back. As you do, you'll discover the fate of the rest of the troopers, help the inhabitants of Aether, and find some new and different types of equipment you can use. In the mean time, there is nothing more to discover behind you so you must continue ahead.