I don't know why but I always assumed it was Captain America who reassembled them to take out the assorted Hydra bases but Thor doing it to get back the scepter makes sense too.
Well, that was the impression I got from the dialogue in AoU -- that the Avengers' mission had been to find the scepter, and now it was complete. Though I'm sure it was a mix of both -- Thor and Cap had parallel goals, Thor to get the scepter and Cap to get Hydra. Natasha was already on Cap's team. And I would assume that Tony came out of retirement as a reaction to the fall of SHIELD, since someone had to take over protecting the world. And Bruce and Hawkeye just tagged along with their pals.