The blue aliens have boarded Destiny before. Spoilers for Sabotage

[Krazeh]

As you say, you can go with overly complex theories, or you can go with the simple and direct.

Claiming that the aliens have been on board Destiny many times before and have had a sufficient length of time there to be able to gain access to systems the humans haven't yet been able to access and gain a sufficiently detailed understanding of the workings of the FTL drive to be able to program around the safeguards to create a overload, but were forced off by a "anti intruder system" of some sort before they could gain full control is not a simple and direct theory. You have to make a number of assumptions and invent a whole new system that has yet to even be hinted at on the show in order to get your theory to fit with what we've seen.

[kwlafayette]

Again, I agree. We know the BA were onboard once when they took Chloe. Between that brief visit and the knowledge they gained from mind probing Rush and Chloe, they were able to devise a method of disabling the FTL drives without computer access and without having been onboard previously.

I don't know, what Rush knows could be pretty thin gruel. What episode did he disappear in? Seems like he was only on board a a few days or a week or two before he got left on that planet. I get the impression he was a prisoner longer than he was on Destiny. Or, he could know a lot more than he is letting on. Kind of a wild card.

PS. Also, I do not think Chloe does anything technical. Beyond basic layout, they would not have learned much from her. I have never even seen her using a console.

[Quadhelix]

I don't know, what Rush knows could be pretty thin gruel. What episode did he disappear in?

"Justice"; he made it back in the next episode.

Seems like he was only on board a a few days or a week or two before he got left on that planet.

From Joseph Mallozzi's weblog:

Craig writes: “BTW, how long after the events of “Justice” does “Space” take place? A day or two? A week?”

Answer: Although it’s never specified, it’s safe to assume that it could have been about a week.

I get the impression he was a prisoner longer than he was on Destiny.

That probably has more to do with the way the episodes were aired, rather than anything actually in the show.

[ONeill4tW]

Someone gained access, to a system that the humans have not yet been able to access. Someone overrode the safeties in the system that the humans cannot access. Someone caused an overload that disabled the ship. Someone did all that in a short amount of time. You can believe whatever you want, but someone staring at the outside of a ship with an unknown computer system in it is not going to be able to figure all that out so quickly.

Hmm... I recall that Rush was able to hack into a completely alien ship... So why can't the aliens do the same to Destiny's computer system?

Anyway, everyone seems to forget that they mind probed Rush. Although he "claims" that he was able to resist the probing, that does not necessarily mean it is true. He was unconscious for most of his stay there. Does he have to be conscious to have his mind probed? Maybe he was able to resist when he was awake but unable when he was unconscious.

He doesn't remember everything that happened to him also, so his account of the ordeal is not 100% reliable.

All the information they would need could have come from him and he is unaware of it. After all they were able to get English out of him, so why not information on Destiny too?

[kwlafayette]

Well, turning a system on and playing around with it while you try to figure it out is one thing. I am not sure Rush got very far with that downed alien ship on that desert planet (plus, an entirely new alien language to deal with). They hinted that the link was not quite entirely one way, remember the three on that same desert planet with the same downed ship, when Zoe told Eli to go back a page? Also, I am not sure how well that mind probe would have worked, unless Rush was not the first human they had ever seen? How would you figure out how to mind probe the first human you had ever seen so quickly?

I think at the beginning, Rush was probably trying to communicate with them (but it would have been gibberish to both sides), and only started resisting once he suspected their intent.

Maybe the blue aliens are the Furling. Who knows.

[escyos]

Well, turning a system on and playing around with it while you try to figure it out is one thing. I am not sure Rush got very far with that downed alien ship on that desert planet (plus, an entirely new alien language to deal with). They hinted that the link was not quite entirely one way, remember the three on that same desert planet with the same downed ship, when Zoe told Eli to go back a page? Also, I am not sure how well that mind probe would have worked, unless Rush was not the first human they had ever seen? How would you figure out how to mind probe the first human you had ever seen so quickly?
.

you mean chloe?