Honestly I don't understand why anybody would reject this???

This adventure would take place immediately after Samus takes off from the surface of Talon IV. Upon exiting the planets surface, Samus decides to take a long rest in her Cryo chamber as her ship autopilots home. However, something goes wrong and Samus’s ship computer hones in on a distress signal. The distress signal is coming from a huge alien vessel (huge like the size of several Star Destroyers) that is drifting out in space. As Samus’s ship approaches the alien craft, a tractor beam activates and the Ship is pulled into one of the gigantic docking bays. As the ships doors close, the gigantic vessel folds and enters a parallel dimension, thus begins Samus’s new adventure…

Upon awakening, the ship appears to be abandoned, there is no power except for auxiliary lights and telemetry from computers. It is up to Samus to unravel this mystery. The mystery being that the ship’s AI has gone mad and the ship is actually a war vessel that is on a collision course with a peaceful planet. It’s goal? The entire enslavement of the race of beings on said planet as well as natural resource stripping as its (the planets) destruction. So in essence, the ship AI has split into several different personalities, and is playing a deadly game with Samus. The Alien inhabitants of the ship are also in a state of suspended animation because as the ship travels through the parallel dimension, the alien inhabitants are being created and refined for warfare until the ship arrives at its destination and assaults the planet…However, the robotic and automated entities are not, these will be the primary enemies that Samus must deal with. In addition, Samus must also deal with the ships cunning AI, who will all the while be taunting her and trying to trick her at every opportunity.

http://www.neogaf.com/forum/showthread.php?t=421019

So, Retro wanted to make System Shock 3?

Sounds interesting, but some of the proposals don't really sit well with me.  For example:

"The main goal for Samus is to disable the engines of the ship, destroy the AI, and eradicate all life forms on the ship. The catch is that even though Samus is all powerful from her previous item acquisition on Talon IV, she will be limited to use them in certain areas of the ship due to the containment matrix that the Rogue AI has set up all over the ship."

Other parts sound pretty cool, though.  It's certainly a very ambitious pitch.  I hope Nintendo expands on this proposal, although it doesn't necessarily have to be in the Metroid setting.

Yeah, definitely sounds nice but I think I would prefer seeing it as an original IP over a Metroid title.

I would have agreed before Other M, but now I think this would be the story driven game the series should have gotten.

I am elated.

This reads like a mash-up of ideas and brain-stormings about some kind of personal dream-project by a developer...

By that I mean that it's incoherent and sometimes overly ambitious. At the end of the document the guy writes he thinks this could be cranked out in a year which to me just seems ridiculous.

Some of the ideas here are definitely intriguing, but others have already been done in other Metroid games like Prime 2 and Other M, and even Hunters. Some of the concept art for those games seems directly taken from this document as well (i.e. the Shock Beast).

Overall, I'd say there is no point in making this game now. At least we now know where some of the ideas in the games following Prime came from. There are a few general concepts that I would still like to see done in one way or another, such as time moving backwards and co-op multiplay.

All in all I think this is just the kind of "brain-storming" document you hear a lot about as projects that are never really made into a game in themselves but rather harvested for concepts and gimmicks used in other games down the line -- think mario 128 for example.

I don't think this was ever intended to be any more than just that - certainly not a finished proposal by any means.

Sounds a lot like Other M: rogue AI, bad things on the ship that you must kill, story driven?

so why not make it?! do it on 3DS! 

In fairness, this wouldn't have been so bad in 2004.

I agree with that.

Here's hoping it still might crop up somewhere.