Its a bit more complex than that, I'm fairly sure the comic has been released now to coincide with the movie, but it is a bit out of date considering Cap is leading the Avengers.
But the basic premise is that Megatron and his decepticons have a new machine that makes them more powerful using super-human DNA. They capture Spider-Man and use him. The rest of the Avengers atempt to save him, only for the Autobots to show up and try to solve things. Then, as UTSHU expalined, they fight but end up on the same side. Turns out
has helped out the Decpecpticons, only for them
I quite like it, it's a good read and it's a bit of fun.