Film Theory: Gandalf Always Planned To Use The Eagles In Lord Of The Rings
2. The Balrog Problem
The eagles themselves are located in the Misty Mountains, so when Gandalf rounds up the Fellowship, that's where they head. Of course they've got to get through the Mines of Moira first, which could have been done to further shroud the real plan in mystery.
Things quickly go to hell while in the Mines, of course, and Gandalf ends up facing off against the Balrog. Definitely not part of the plan. Fighting for his life against a 50-foot beast while orcs are closing in around him obviously puts the wizard in a little bit of a sticky situation at this point, as if he dies then the agreement with the eagles dies with him, while outright revealing it to the rest of the Fellowship would put the whole enterprise jeopardy.
Knowing he's about to be dragged into the abyss, then, the theory posits that Gandalf used his final words to the Fellowship to hint at the plan without giving it away completely to the nearby orc, saying:
"Fly, you fools."
The subtlety was perhaps a bit lost on Frodo and co., but to their credit they have no reason to take the farewell as any form of hidden message. Plus their friend and mentor literally just died in front of them, so they're probably not thinking his words have a deeper meaning more than "get the f**k outta here!". Consequently, the Fellowship continues to follow the cover plan: getting the ring to Mordor by any means possible.