Spoilers for GI Joe - if you don't want to know what happens, don't read X-p
1. Soundwave recorded the whole fight between the Joes and Cobra.
Miffed that these puny fleshlings have used Megatron's technology to this extent/that these humans actually begin to become a threat to the Cons/think of themselves as the most technologically advanced factions on Earth, Megatron and his army declare war on both factions. There's only enough space for one secret war on Earth, and that will be the war between Cons and Bots, not GI Joe and Cobra.
(I really, really want to see Screamer VS that strange flying vehicle of Cobra. That would be an awesome battle).
2. This strange flying vehicle that appeared right at the beginning of the movie?
Am I the only one or did that thing look quite similar to Megatron in ROTF?
Are there connections we don't know of (yet)? Or is Megs using Cobra to weaken the humans and their governments?
3. When Ripcord destroys the last missile, the nanomites spread over the Nightraven - just this time they don't destroy the jet and are eventually lost in space. Ripcord believes that Destro programmed the nanomites not to destroy his toy and decides to keep the Nightraven as a souvenir, not knowing that he just has gained Pandora's already opened box.
The Nighthawk is Starscream, a scientist turned Decepticon from the planet Cybertron.
The young, intelligent Seeker concluded just vorns after the beginnings of the war on his home planet, that this whole confrontation would have no future. Not willing to die with his planet, he conviently gets MIA after one of the harder battles and, after a long journey, lands on Earth and takes an interest into the dominant species, the humans.
He decides to study them and, as a Decepticon, soon begins to orchestrate the world events, seeing the humans as his personal social and evolutionary experiment.
He was the real inventor of the nanomites and programmed them not only to not destroy Cybertronian alloy but every thing that has his Spark signature as well. He was the mentor of Mindbender and Cobra Commander and is now waiting for those two to break out to unleash his newest round of "tests" on his specimen.
a) One night Screamer has to stretch his legs - and is promptly discovered. He manages to tell GI Joe a sobstory about a war, how Cobra Commander managed to enslave him somehow and how he was freed by the destruction of the underwater base and the controlling device within. He claimed to not having revealed himself before, because he was afraid that the humans would harm him again. Do the Joes believe him?
b) Cobra Commander and Destro break out. Now it's time for Starscream to return to his loyal followers.
c) After the battle with the Fallen, NEST and the remaining Autobots are surprised by a sand storm on their way back home, they have to land and are grudingly accepted to stay in the pit until the storm is over. Now, naturally Screamer is discovered and must find a way to explain why he's on Earth and what he was up to for the last several thousand years.
d) Screamer was really enslaved/used by Cobra and just studied the humans from afar, without manipulating them at all. He run away from Cybertron because he became aware that he had made the wrong choice and was to scared of the Bots to defect. Now, he either reveals himself to the Joes, wanting to thank them or he's discovered by the bots like in c).