Idea for Metroid Prime 4 story

I was thinking about the timeline-switching concept I came up with based on Kensuke Tanabe's comments on how he might consider something jumping across the timeline, and followed up with a thought on how to tie the Prime series into the main series. Here's the idea for the storyline.

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It Begins

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"Metroid research center infiltration detected. A Metroid egg has been stolen and the infiltrator has escaped."

Cut to Samus in her ship, reviewing security footage. A blurry figure having a shootout with Federation troops in a ship hangar, apparently being able to teleport around as he fights, decimating the troops.

A light blinks on Samus's display. "Federation-tagged Metroid DNA detected. Target is in the area."

As the ship enters the atmosphere, and camera shows an expansive alien surface world, the title is shown.

The ship touches down and control transferred to the player, who is introduced by non-interrupting text-only tutorial on scanning, lock-on, morph, etc. as the situations come up. To immediately introduce the "labyrinth exploration" aspect of the game, there are immediately two branches off the main path, both of which must be briefly explored (with their own short little tutorials) in order to unlock the main path. (This is in contrast to the original Metroid Prime's intro sequence which is a linear gauntlet sort of thing).

The player soon encounters Sylux and a fight commences. As expected from the earlier security footage, he teleports around. The fight pairs as a tutorial on combat movement mechanics. Getting off a single good shot at Sylux, he drops the capsule containing a baby Metroid. He picks it back up and decides to run instead of continuing the fight, opening a portal in the process that Samus chases him through.

On the other side of the portal, it appears to be the same place, but now it looks like a Metroid hive.

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It gets more interesting

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See the link in the preamble for how the mechanics of the game progress, but it turns out the Metroid Hive environment is a time-altered present, and Sylux had jumped decades into the past.

Sylux's mission? To deliver a Metroid to the Space Pirates that had been modified to eliminate its weakness to cryogenic weapons.

His motivation? To destroy the Federation that had sent his brother on a suicide mission, and thus save his brother and end the organization's corruption. Plot twist: His brother is Adam Malkovich, whose death had been faked so he could lead a ghost/black-ops squad -- the squad Samus eventually works with in Other M.

The irony is that in the alt-present, the Pirates didn't just destroy the Federation and go about their business, they went on to conquer everything. And it was all thanks to Sylux giving them the means to create an unstoppable weapon.

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The conflict

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In the past, Sylux has already delivered the modified Metroid to the Space Pirates, but they haven't completed the process of weaponizing it yet. Samus determines that if she can destroy the source Metroid and all its descendants, she can save the present.

Sylux decides that destroying the Federation is more important than saving his brother, and chooses to remain Samus's enemy and to stop her from reverting the present to its former self.

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The Resolution

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Samus is able to kill all the descendants, but can't hurt the source Metroid who has evolved to a Queen. Nothing works, not even the power bomb from the inside.

However, in the alt-present, the Queen is still in the same place. Jumping back and forth in time and using local chrono-distortion (again, see the mechanics from the link at the beginning), Samus is able to get the alt-present Queen to kill the past Queen.

The resulting time paradox collapses the past and alt-present, restoring the timeline and destroying the planet's ability to support time travel.

Against her orders to kill Sylux, she apprehends him instead and hands him over to the Federation to stand trial. Upon reviewing the footage recorded by Samus, the Federation gives the order to exterminate all Metroids because of the galactic threat they pose.

The extermination order leads directly into Metroid II.

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TL;DR

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Samus chases Sylux back in time. Sylux in the past gives a non-ice-weak modified Metroid to the Pirates, changing the timeline so in the present the Pirates have conquered everything. Jumping back and forth between the alt-present and past, Samus gets the alt-present Queen Metroid to kill itself in the past. The events of the alternate timeline convince the Federation to exterminate all Metroids, tying it all into the main series.