The game is separated in Chapters like in Kid Icarus: Uprising but Chapters work slightly different this time around (more on that in the gameplay section).
Chapter 1 - Enter Aetos!
The first chapter starts with Pit flying around and doing various acrobatic tricks in the air before Palutena reminds him that he's using the Power of Flight to arrive at a specific location, not show off, Pit apologizes and asks Palutena to remind him of the location he needs to go to, with Palutena replying by telling him that it's the "Garden of Lightning", a garden located way up at the top of the gigantic "Mt. Olympus" which goes way over the clouds, Pit arrives and finds a young man taking care of a group of small golden birds, "Aetos", he asks for the package he requested and Pit gives it to him before asking about why didn't he just call the Mail Angel, to which Aetos replies by saying that the package he requested is very important and people would try to steal it, shortly after that a group of pirates drop from a giant zeppelin and attack the gardens, Aetos flies away with his birds and Pit is left to fight off the pirates.
After defeating every pirate in the gardens Aetos comes back with his birds and explains that the ones who attacked were part of a gigantic gang of sky pirates known as "Clippers of the Clouds" that have repeatedly attacked the Garden of Lightning trying to steal Aetos' golden birds because of their shiny gold feathers, and that he's grateful that Pit protected the package as it's very important, Pit opens the package and finds out that the important item is.....seeds, Aetos explains that the seeds are actually very rare seeds and it's the only thing that the gold birds eat, and that the Clippers of the Clouds may have wanted to get them to lure in the golden birds, Aetos once again thanks Pit and feeds the golden birds after he leaves.
After that we get a cutscene of Aetos talking to a giant man sitting in a throne in the thunder clouds, Aetos reveals the man is "Zeus", his boss, and tells him of the attack at the Garden of Lightning, Zeus asks what did he do and Aetos says that he ran away to protect the bird while Pit saved the garden, Zeus gets mad at Aetos and scolds him for having to rely on an angel from Skyworld to save his gardens, Zeus mentions that this isn't the first time something like this has happened and sends Aetos off, who goes back to the gardens, where he starts crying.
After the cutscene, we cut to Pit a few days later being called by a worried Aetos who tells him that he needs to get there as fast as he can and that it's an emergency, Pit starts flying over to the Garden of Lightning but in the process sees a group of golden birds dashing away at incredible speeds, one of them almost hitting Pit, he manages to arrive at the Garden of Lightning and finds a sobbing Aetos laying in the floor being held down by a destroyed pillar, Pit helps Aetos back up and he then explains that the Clippers of the Clouds attacked, destroyed the garden and scared off the golden birds, and asks for Pit's help in retrieving the birds and stopping the Clippers of the Clouds before they get their hands on the birds, Pit decides to help Aetos and flies off in the birds' direction, where he finds the Clipper of the Clouds' zeppelin, which the main engineer, who chases after Pit in a smaller flying ship, refers to as "Grand Ferdinand", Pit asks what that means and the engineer starts ranting about how "younglings these days know nothing about history" before revealing his name, "Hinderburg" and calling troops to attack Pit with their own ships, Pit takes most of them down and tries to get one of the birds but Hinderburg fires a missile that hits Pit and sends him plummeting straight to the ground, once he lands he opens up his hand and finds a small bit of a golden feather in his palm before Pautena sends him back to Skyworld, saying that "it's just what they needed".
Chapter 2 - Under the Ocean!
The game plays very similar to Kid Icarus: Uprising but with controls tweaked for the Wii U, the game is split in flying segments where one controls Pit as he takes down enemies in the air and in land segments where Pit takes out enemies brawler-style in the ground, however the game introduces several new features to make it more unique.
First of all, Chapters work differently, they now can be accessed normally through Skyworld like in the first game but you can do them at any time now, and while you're not doing a chapter you can explore lands you've been to since land environments are now more open.
You can explore areas you've already been to or "Soar", a proccess in which Pit chooses a location in the new World Map and Palutena gives him the Power of Flight to get there, in the process blasting enemies in his way, while Soaring and exploring past locations sometimes Events may happen. In land, Events occur randomly but if a past location has an Event going on it will be marked by a "!" next to the location, in the sky, an area might be marked by a "!" in the World Map and if you Soar to that area you'll get the Events, these can range from tougher enemies, more loot, and more.
Another way to get new weapons is to beat up enemies to get "Materials" which can be crafted into new weapons, some weapons can only be obtained by crafting them out of materials dropped by enemies. Every material you collect is automatically saved in your "Inventory", which can also be used to save healing items for later missions, as well as stat upgrades and other items.