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hmmm.... a machine.... but no dark skies.... where did the clouds go? your thoughts?

they just flew higher then the black clouds. them notice the trail of dark cloud that its draging.

That'd be my guess as well

yeah, cause you can see the clouds below in another spot, or trailer...and theres a sunset...

It looks almost as if the hovercraft is smoking out the rear too...

it is possible, b/c the ship is almost falling, and it doesnt look on...

As I mentioned in an other thread, The Logos (not a machine) looks in bad shap, the hover pads are not on, and it is smoking (and also draggin some smoke, but you can see the difference in motion)

The hovercraft is above the main cloud cover, which is why the sky looks normal.

As for the condition of the craft, it moves by too quickly for me to tell.

The answer to your question can be found in the M1 and the animatrix.