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Ok, I'm gonna come up with some half-assed reasons on how Samus lost all her equipment.

Metroid 1/ZM-Prime

Samus returned to Space Station Minerva (predecessor to Ceres) after beating Mecha-Ridley on Zebes. When she got there, she let the researchers have her suit so they could find out how many of those things worked. So, Samus left to her home or w/e. Anyways, while they were experimenting with Power Bombs, a Space Pirate attack rocked the station, setting off the Power Bombs. Samus happened to be nearby, and went to investigate. When she got there, she killed the Space Pirates, and talked to the only remaining scientist left. They were able to finish testing on the Missiles, Morph Ball, Bombs, Charge Beam, and the Varia Suit. They gave her back her suit, and also told her they installed a Grapple Beam, a piece of technology they had been working on for some time. Anyways, she took the only ship not damaged by the Power Bomb, and set off to find the Space Pirates new headquarters. She got the distress signal, Metroid Prime happened, yeah, we all know.

I'll do Prime-RoS later. Praise wanted, critiscism expected.
Thread title: 
Not bad. Here's my take:

In 2000, a group of programmers called Retro were working on a 3d sequel to Super metroid when suddenly it became time to program the starting level. An intense debate began on the format of such a level. An aged, wised voice broke through the din:
"Let's give the player some of her abilities at the beginning, so the newbies can figure out how they work!"
This sage idea was welcomed by all, until fierce contention broke out about which powers she should have. After much hard work and conference, it was decided that she should not be as high-powered as she was at the end of Metroid. Now there was peace in the studio, and the team began work on the frigate.

Can anyone contradict me? I don't think so.
Hey, don't knock his idea.  We like discussing what happens between Metroid titles, without people like you saying "OMG IT"Z ONLY A VIDIO GAEM LOLOLOLZ!"
Quote from ShadowMagus:
Hey, don't knock his idea.  We like discussing what happens between Metroid titles, without people like you saying "OMG IT"Z ONLY A VIDIO GAEM LOLOLOLZ!"


no..metroid is our world,we want to know EVERYTHING of all games...
I thought that's what I said...?
Quote from ShadowMagus:
I thought that's what I said...?


oh,i think i read too fast  :?
You're right shadowmagus.

I'm sorry chinchilla.  :(
All is forgiven.  Wink
*manly poses*
Wow, first logical explanation (sp?) I've seen.  Wink
PAGE BREAKER
Ready and willing.
Gah. We all know the Space Pikachu steal them while Samus is flying around in her ship. Come on, n00bs.  Wink
But Space Pikachu is soon fried by Space Mario, who takes them to the princess in a vain effort to score.
Maybe Samus' suit has a range? You know maybe some of its functions only work so far away from Chozo Temples? So when she moves away too far they deactivate.

[unlikely] Maybe Samus decided that she didn't need them anymore so dumped them [/unlikely]

[likely] Samus has had other missions between games, possibly another Tallon IV type explosion disabled her suit[/likely]

The researchers idea is a good one. One question though - How the hell could they read Chozo!?!?

Samus ORIGINAL suit couldn't even translate items in ZM how could the Feds?


Maybe Samus is going to surprise us by letting us know that she has been stockpiling a pile of items and suits! FOR A METROID RTS!!! A Real Time strategy game with dozens of morph ball items and plasma beam upgrades!!!!..............


.........or not....
Ok, now for Prime-RoS:

Samus, after leaving Tallon IV, went home to relax. However, 6 months later, Samus got a call from Space Station Juno, saying they had just lost all of their research teams on the planet SR388. The last team sent down sent a transmission before their destruction, saying that it was Metroids who had attacked them. The Federation gave Samus a mission to go exterminate all Metroids living on SR388. However, they cautioned Samus that the Metroid on SR388 were different from the ones she found on Zebes and Tallon IV. So, Samus went down and found a Metroid Larva. However, right before her eyes, it mutated into an Alpha Metroid, and nearly killed Samus. Luckily, she was close to her ship, and was able to make it back to Space Station Juno. Unfortunatley, her Power Suit was heavily damaged from her encounter with the Alpha, and so they sent it to Space Station Vesta (I hope someone is noticing the Roman Goddess trend here) to repair it. Samus also went to Space Station Vesta because they had apparently discovered some new data on the Metroids. They found out that Metroids evolve, which is what Samus saw on SR388. After Alpha, they become Gammas, then Zetas, then Omega, and there's even a Queen. However, after learning this, a distress signal was sent from Space Station Juno. The doctors told Samus her suit was all fixed, but it was heavily damaged and the only working things were (insert name of abilities Samus had at the beginning of RoS which I don't know.) So, she went back to the Space Station Juno, and found that a Metroid egg had been in her suit for some...strange reason, and it hatched on Space Station Juno, killing everyone, and knocking out the controls, causing the Space Station to drift out into space, and then self-destructing. How she learned that, I don't know. But it did. So, Samus descends upon SR388, Metroid 2 happens, yada yada yada.

Ok, the gap between RoS and Super Metroid seems to be about a week, so I can't think of much there...although I probably will come up with something. And we all know what happened between Super and Fusion so no point doing anything their. But I might come up with something that has to do with Samus and Adam...I smell Fanfiction...
Pretty good... thing is, that wouldn't be an official explanation ever... If it was, I'd be annoyed. I mean, Samus' upgrades being damaged by a freakin' alpha metroid? I didn't even understand how the tiny blast in Orpheon could destroy so many components. Come on, Samus' been fried by Mother Brain's hyper beam, tail-whipped by Ridley and stomped on by the Omega pirate soo many times, and we don't see her shoulders falling off from that. What could a tiny little shockwave or a slimy alpha metroid do?

I'll never buy the "oh, you're so damaged we need to remove everything" thing. And don't mention Fusion, that was because of infection, not actual physical damage.