This story follows the canon timeline of the story. This means that the order is Metroid, Metroid Prime Series, Metroid 2: Return of Samus, Super Metroid, Metroid Fusion. According to the War Naming of the story, these are known as The Zero Mission, The Phazon Crisis, the Metroid Crisis, the Space Pirate Eradication, and the X Incident. Also, since this is a Halo/Metroid Crossover, you will be noticing several Haloid references, particularly in the Master Chief versus Samus scene.

Chapter 1: Forward Unto Dusk

Samus Aran looked blankly around herself. She simply stood there, examining herself in a half-broken mirror. She was as she has always been, for the most part. As she stood before her shattered reflection, wearing only what undergarments she'd brought along with her for this mission, she could see the scars of years upon years of battle. Her eyes were a magnificent blue, not of the ocean or the sky, but of icy daggers. Some said she could kill with a glare. Her flowing blonde hair was a waterfall down over her shoulders. Her muscles were tense, and defined from years of training, and fighting.

And yet, something had changed after her last mission. Her skin had become more pale than usual. Normally she would not be concerned, but she could feel it. There was an "other" presence inside of her, which hadn't been there before. Samus Aran X had been a menace for a very short time, and yet she had been a terribly clever enemy. SA-X had possessed a power that almost rivaled Samus herself. Only once before had Samus ever faced an enemy as difficult as SA-X, and that time had also been somewhat of an offspring of Samus.

Samus shuddered at the memory of her Dark counterpart. Dark Samus had been the most terrible enemy Samus had ever faced, and Samus had had one too many scrapes with death during the Phazon Crisis.

The Phazon Crisis was the name of one of the many "wars" Samus had taken part in. Although the Phazon Crisis had been years ago, it had burned a whole in Samus' mind ever since.

Samus slipped into some light, civilian clothes, and stepped back into the cockpit of her ship. ADAM's voice appeared over the intercom. "Lady, the Federation has sent a message with the title "Urgent" during your brief bathing period. Would you like me to play it for you?" the computer questioned. "Yes," replied the Hunter, who sat at her console. As she did, a man wearing a Federation Commander uniform appeared on the screen. Behind him was a man wearing a uniform bearing several medals, although Samus could not easily recognize them as official Federation medals.

"Attention Samus Aran: due to your recent disobedience aboard the research ship, BSL, you are being presented with two options," said the man with a stern tone, "You may either serve your time in a federation prison, or help us resolve an issue which we are being asked for assistance in. Should you choose to decline, and flee, you will be issued a warrant, dead or alive." Samus gritted her teeth as two options appeared on her touch-screen. They read a simple "Yes" and "No". A small force in the back of her head urged her to simply flee, and kill anyone who got in the way.

Samus clicked "Yes".

The transmission began again. "Congratulations, Samus Aran. We would like to thank you for siding with the Federation and its allies," said the man, with false happiness, "I would now like to turn your attention to Fleet Admiral Lord Terrence Hood, of the United Naval Space Corps. Lord Hood?"

The man stepped forward, and his facial features became more apparent. He was an aging man of at least fifty years, and he stood with a rigid posture typical of military men. "Miss Aran," he said, "the UNSC is a military presence from a planet in the outer rim of the Galaxy, called Earth. For centuries, we believed ourselves the home planet of the human race, and although we now know this not to be true, we still defend her like she was our mother." Samus reclined in her chair, and continued watching. "I'll cut to the chase, Miss Aran," said Lord Hood, "I'm requesting help from the Federation with a growing problem called the Covenant. I'm assuming you've only heard a little about them. Recently, the Covenant began a massive and zealous genocide of any humans they could find. Although we've managed to kill all of their leaders, the Covenants' still functioning in several small pockets of resistance. These pockets have been launching rather effective gorilla warfare attacks on our bases for days now. We want you to go to the planet Virgil II and eliminate any covenant you find. I'd start with the city on the middle of Virgil II's largest continent." A map appeared on screen, and downloaded into Samus' Power Suit. It pinpointed a small area in the middle of a giant landmass. "We are counting on you, Miss Aran." The screen cut off, and then there was blackness.

Samus stood from her chair, and grabbed her Power Suit from the tube it was suspended in. Her suit had gained a few unique abilities from her most recent voyage to BSL: namely the ability to switch it's function from a selection of all the suit upgrades she'd ever obtained. As she slipped into her suit, she ignored her instinct to run. She stepped back up to the controls wearing everything but her helmet. "ADAM," she commanded, "set a course for Virgil II. Let's get this over with, so that I can get the Federation out of my hair." ADAM took control of the ship, and gave an affirmative "Yes, Lady."…

… Elsewhere, Lord Hood stood before the Federation Commander. "Do you think she'll succeed? After all, she doesn't know that we've just sent her into the largest pocket of known Covenant rebels," queried Lord Hood. The Federation Commander gave a sly smile. "That woman has participated in more one-human-wars than anyone else on the Federation Records. She's single handedly cleared planets of large and deadly adversaries which no one else has survived against, and she's killed the Space Pirate command twice," replied the Commander. "That's not what worries me," said Lord Hood, "It's the fact that my men have just picked up a transmission from Virgil II written by one of our AI that we thought to have been lost outside the Galaxy. Accompanying that AI is a living legend among our men. If those two mistake each other for enemies, there may not be anything left of them, or the city, to recover for reconstruction efforts." The Commander stared blankly at his screen once more. "Anyone that can kill Aran deserves a more medals that either of us have combined, Lord Hood. Believe me, in the unlikely event that those two clash, I can almost assure you that it will end in a stalemate," informed the Commander. Lord Hood gave the man a skeptical look. "Almost doesn't quite tickle my fancy, if you get what I mean."