AN: I had this idea for a while and now, it's time to put it down! This takes place after the events of the first Prime game.

It's been a year and a half since the defeat of Metroid Prime on Talon 4. The galaxy, as the renowned bounty hunter Samus Aran knows it, is at a relative standstill and peace. There were no more readings of any Metroids nor any Space Pirate activity so she took this time to get some R&R. For the past few months, she allowed her ship to drift lazily through the cosmos, stopping only for gas, food, training, or a bathroom, since her gunship didn't have one installed. She kept reminding her to get it installed one of these days but she kept putting it off.

Another lazy day came and while her gunship navigated itself through the stars, Samus herself decided to catch some z's in her seat. She admitted to herself that she has been getting a bit lazy in these times of peace but she couldn't pass this up. As she was dreaming of the past, she received a call via her transmitter. She jolted out of her sleep and quickly got herself together. She looked at the screen to see who was calling: It was the Galactic Federation Unit located in the Delta Asteroid Belt Sector. She was drifting near that part of the cosmos. She answered the called and a voice came from the intercom.

"DA to Aran, DA to Aran. Do you read me?" The man on the transmitter asked, coming in loud and clear.

"This is Aran. I am pulling into your vicinity for supplies now."

"Good, restock as you please. However, since you are here, we have an idea for you, Samus."

This piqued her interest as they might have something for her upon entry. Buzzing back in, she asked...

"And what would that idea be?"

"Report to the main conference hall for briefing. We'll fill you in on the details there." And with that, he hung up. Samus sat back in her chair, deep in thought about this.

Maybe it's a new prototype weapon they want me to test? A mission? I have been inactive for a while...

These thoughts flooded her mind as she docked at the bay on the east side of the colony. Knowing this is a GF monitored sector, she deactivated her Power Suit and unboarded her ship. She was greeted by a welcoming party: a group of soldiers saluting her. She saluted back as she began walking inside of the colony. A soldier accompanied her as she makes her way to the supply room.

"Great to see you again, Samus. We thought something happened to you since you went silent."

"Nah, I was just...silently bettering myself." Sleeping her days away she meant but he didn't need to know that. She chuckled.

"Well, we will be needing your assistance in this mission." Well, there goes her vacation. At the same time, however, she was glad she can finally get some action in.

"Is it another Space Pirate reading? Does a docile species need assistance in surviving?" She asked, trying to get some details. The pair arrived in a big circular round filled to the brim with humans and other creatures sitting around a podium. The guide led Samus to the podium as the general of the sector of the Federation, Sgt. Larson, approached the bounty hunter. He looked to be in his late 40's. She saluted as he bowed.

"Great to meet you at last, Aran. Adam Malkovich told me a lot about you, so I'd knew you'll be right for this job." He grinned, putting his briefcase down on the podium.

"So you know my former commanding officer? Great to know...I think. Let's just get to it: What is this mission you all meed my help with?" She asked, standing against the podium.

"Very well. Turn your attention to the monitor." The pair along with the audience looked up at the monitors. The video feed picks up to a grassy field with some life Samus never seen before. In the distance, Samus sees a group of...black and purple dots coming from the ground. These dots then began to take shape and transformed into one of the beings that were still in the scene. After it's short transformation, it attacked the other beings in the video. There were some gasps and crying in the audiences, but being used to this, Samus just watched. After the massacre, the video ends.

"Those...purple ball creatures..." Larson started, turning back to Samus. "We dubbed Shadow Bugs. They have the ability to morph into any living organism and become incredibly violent and destructive. Their endgame: the complete destruction of every planet they come across. They achieve this by traveling to the core of the planet and corrupting the flow, causing it to explode." The projector then cut to 4 planets. "We recently captured one and with the DNA we've got from it, we were able to pinpoint the planets the other Shadow Bugs are on."

"So go to those planets, exterminate them before they reach the core. Got it."

"Hold." He told her before she could walk off. "There are a few more things we need to discuss, Aran." She sighed and turned back to him.

"Few things. First, you can't really 'exterminate' them. More like, imprison them back into their first state as eggs." One of the assistance came from the back room to show her one as an example. Its encapsulated in a protective glass. It was a deep purple egg radiating powerful energy. Samus got a closer look at it.

"Are you sure it won't break out of its egg and attack?"

"Yes. It is powerless in this state unless someone releases it. Secondly, due to the seriousness of this mission, we have decided it's best you have some help."

Samus raised an eyebrow. She always loves doing missions alone and being alone in general so this proposal isn't sounding tempting. "Help, what kind?"

"We have assembled a team for you as well as a new gunship to accommodate you all." He explained, receiving a groan from Samus.

"Really?"

"Yes, really. Let's go meet them, shall we?" She reluctantly nods and follows him off the stage. They both went down through a series of hallways. As they walked, Samus's mind raced as she went over all of the new info.

Shadow Bugs? The ability to destroy planets? A new freaking team?

"We're here!" Larson spoke up, shaking Samus out of her trance. "We have scooted them from different worlds, I think they'll be of great use of you." He unlocked the door and Samus walks inside, mentally steeling herself for anything.