"Attack on Titan Season 2 will see major changes to the story line as soon as it gets back. While fans of "AoT" thinks that the upcoming season will focus on the manga series, recent reports have already made it clear that the next season will be a separate story.
While there are still no confirmation on how the story line would be or if it would continue the events that unfolded during "Attack on Titan" Season but it can be concluded that it will still unravel the mysteries of the Titans inside the walls.
There are reports that "Attack on Titan" Season 2 would feature the stories of the manga series of the "Clash of the Titans" and the "Uprising." However, there are clashing reports as well that says that "Attack on Titan" Season 2 would be different from the manga series.
"Clash of the Titans" may sit well with the upcoming "Attack on Titan" Season 2 since in the promotional poster of "AoT" the Colossus Titan is featured as he tries to break into the walls. The anime may just continue the story of the first season while still revealing more of the story of how the walls came to be and where the Titans came from.
While "Attack on Titan" Season 2 may also get its story line from its manga counterpart as there are good stories to tell in the "Uprising" especially with the storyline of Eren and Historia being abducted by Minister Nick.
If "Attack on Titan" Season 2 would follow the manga series, it is definite that they will not run out of stories to tell. However, reports are saying that "AoT" will stand on its own and will be different from the manga series.
Fans of "Attack on Titan" Season 2 would still have to wait for further confirmation about the real story line of the upcoming "AoT." But it won't be long as the upcoming anime will be back in the first quarter of 2017.