Just run the basic story idea past me again please. Thanks.

I was honestly hoping someone else would do this, but I guess not.

Not final, but pretty much this:

A crew of space explorers were traveling to a distant galaxy when their ship was hit by space junk. Before their ship exploded from the damage, the crew managed to flee in escape pods but end up getting seperated. and land in a nearby planet. This planet's natives were known to have destroyed themselves and all intelligent life in a great war long ago. Now, only ruins remain and the only somewhat surviving structures are giant war bases that are loaded with traps and explosives. The crew must escape these giant bases and meet up in a planned rendezvous point.

That's a summary Quirvy gave on the old forums. I think there is a larger version somewhere, but I haven't found it yet.

Edit: And these are the characters:
-Captain:  Floyd the wolf
-Pilot: Felix the eagle (with a robotic arm)
-Navigator: Jean the cat
-Technician: Ivan the gerbil
-Medic: Rita the armadillo

And the bonus character:
Janitor: Hugsy the mentally disordered hamster
While the airship is crashing, all the crew members get off with escape capsules. After beating all the sets, it turns out that Hugsy stayed on the ship and crashed on the moon.

Yeah, that'd be the one I just posted, which Accel gave.

Also a fun trivia, how we came up with the names of the characters:

Where's Katrina?

Er, instead of finding a place to meet up, say they need to repair the ship and get some special parts from weird dungeon-like places. But that's kinda like MRR, and that's TNT-involved...

Cheers. It's just that I'm reading a book on how to write games and I thought I'd have a go at setting up my own version of how the game runs based on this story you have. Who's the main character?

All of those characters have their own set. So I'd say the five crew members are equally "main". But if I had to pick one, I'd say that Floyd the captain is the main character.

And the ship crashed on the moon with Hugsy. There is no way to repair it as it isn't there. Instead, I think they should find an abandoned spaceship in the abandoned city.

Are you saying that you alternate between playing characters between levels? And does this crack team of space pirates follow you around throughout the game? If so, wouldn't this be detrimental to the gameplay? On the other hand, you could swap between characters like in HATIC and then use this to solve puzzles. Each character could have strengths and weaknesses and the player would have to figure out how to use them to maximum effect. Do you know the whereabouts of the full details of these characters?

Each of the 5 characters land in a different location on the planet. From the very start, you can pick 5 levels, one for each character. When you beat a level, you can play the next level for that character.
So at the start you would have levels 1-1, 2-1, 3-1, 4-1 and 5-1 unlocked. If you play through several of Floyd's levels, you have say up till 1-6, 2-1, 3-1, 4-1 and 5-1 unlocked. If you now play 2 of Rita's levels you have till 1-6, 2-1, 3-1, 4-1 and 5-3 unlocked. The 5 characters don't join up till the very end of the game.

That's an interesting concept. And there's no solid story for each of these characters in place at the moment? We know how many levels, but we don't know what they're going to be doing in the levels?

They're trying to meet up again in the central city. I suppose they saw it from the launch pods. And to do that they have to find their way through abandoned military bases.

I'll try and jot down some ideas for a storyline based on what you've told me.

Remember, this is a simple flash game. We don't need a Final Fantasy-esque story. Gameplay is the most important part.

Agreed. But this is partly for my own entertainment; I don't expect much or any of it to be used. It would be good if there was a basic story behind Aeon though. At least more than the virtually non-existent story in HATPC; that was almost arcade-level story-telling!

If the game is taking place in futuristic war bases, are arrows going to be replaced with something more up-to-date like laser boxes or something?

Another idea: there should be an opening level where all six characters are present and the player has to control one while the others follow around the crumbling spaceship to the escape pods. There are no real traps, but the ship is collapsing around them. That'd be a cool way to start the game off. Very cool.

Another idea for the end is that once the characters meet in the main area, there is one last level with each character. They find signs to the ship hangers where they find a elevator. At the top, they are in a room storing a ship the size of the starship enterprise d, if not larger. However, to relase the gangway, they must get access to the bridge. The last level is where you play as the gerbil and must crawl through small pipes. Another idea is that they find enough food to support their lives, and the bonus levels are where you beam the hamster onto the ship to reach the bridge in the last 5 bonus levels.

Arrows are most likely going to replaced with missiles. They are futuristic, are more likely to be shot out like that when released from a crate and they are more likely to destroy stuff upon impact.

I like the idea of a tutorial set where you control the 5 main characters as they try to escape the ship. But Hugsy shouldn't be revealed till the final set.

And yes, one of the ideas was that there should be a final set inside the city where you control each of the five main characters as they make their way to the ship.

For the last levels though, the plot should be where the main characters must navigate towards the ship. However there are obstacles that block them such as:

Hydraulically sealed doors.
An elevator that must have a motor replaced.
ID card scan to disengage force fields blocking the ship.

However, only one character can go to to that area with the ID/button/backup motor for reasons such as:

Powered down pistons that will crush anyone but the armadillo with it's hard shell.
High up vent only the eagle can fly up to.
Speed trap only the wolf can run through.

There doesn't even need to be much plot. For example, the hamster must crawl through tunnels to retrieve a map, then after a bit of walking, they reach the ship assembly area where a collapsed ceiling makes the only way out from under pistons that only the armadillo can survive. Then, all the pistons are lifted so they can get through. The cat does something to open up the hydraulically sealed elevator, and when it breaks at the top, they break the elevator's top and is able to escape, but there is a guard dog that only the wolf is strong enough to face. After installing a backup motor, they get out and last, the eagle must fly to the ceiling and shut off the shields that block ship access. The end.  

wait should we come up with a reason why the last levels will be more difficult? maybe b/c that city used to be a heavily-guarded capital or something....

I have a cheap idea for the story-telling: You start a new game and you see a black screen with text coming up as if someone was typing, and you're reading the captains log as he sends a frantic report from within the falling escape pod to the other pods. And while reading it, everything shakes every once in a while and upon impact you get that static screen. (would be cool if it had sound....) Then it goes to black again, and the black slides away as if it was a door and then a bright flash from the light outside, and then that flash quickly fades into Tutorial 1, and you're standing there as Captain Floyd in the level next to the pod (not at the start screen).

cheap, simple, short, straight-to-the-game, and kinda cool

Or he sends out an SOS message where he explains stuff. In the background you hear beeps as in morse code. In the end the message stops mid-sentence and the beep turns into a long high note. After that you start in Set 0, the tutorial set, which takes place on-ship.

Another idea that was used in a horror game is that it displays text on the screen beetween levels and at the beginning and end of the games. In the end, you learn that the text is an e-mail. Instead, the story could be told as not only captains logs, but diary entries and letters sent later on. At the start for example, it could say this:
Captains logs
Date:<insert date of game here>
This will be the last log entry of captain Floyd as captain of the <insert ship name here>. We were sent as one of the first probes to investigate life and other important information in the Andromeda galaxy. The first ship, we are responding to a distress call now. We believe they are near a planet codenamed HAF352.

Of course this isn't official but I think that the story should be that the ship is one in a fleet of three or more in another galaxy, each having a crew of six, and responding to a distress call, they are shot down by a military turret. The shot, despite them getting out of the danger zone, makes them forced to use the escape capsules, each which due to navigational damage, is accurate only to 30 miles. Or is there already a reason for the damage?

I won't like anything that complicated. The ship should just get hit by an asteroid or something and it crashes to Aeon. I have my doubts about the SOS message as well.

I recommend this book: http://www.amazon.com/Ultimate-Guide-Video-Writing-Design/dp/158065066X
It gives some quality tips on how to write games and design the ups and downs of levels. Good read too.