On Quantico Season 2 Episode 21, Owen realizes that the cache has been deleted and taken offline, like it never existed. This means that the collaborators are ready to enact whatever plan they have up their sleeves.
When Owen goes to rally the team, Ryan and Raina aren't interested. This prompts the task force to bring Matthew Keyes, Will Olsen, and Miranda Shaw. Like Alex says, they are going to need all the help that they can get.
In order to figure out what the collaborators are planning, the task force takes a look at President Roarke's executive orders. Will figures out that the collaborators plan to hijack planes. They are going to make it appear as if Muslims, who are on Roarke's Muslim registry, were terrorists, when in fact the truth is that the collaborators hacked the plane via cell phones. It turns out apps can be dangerous.
The task force divides and conquers. Alex goes to Alice Winter to figure out what flights and passengers are being targeted. In order to get that information, she has to blow her cover and attack Alice.
Shelby goes to Clay to have him use his connections to get the Presidential override code so that Miranda, Owen, and Will can give it out to the pilots to get them to emergency land their planes.
And Raina? She turns herself in voluntarily to distract the FBI agents who are at the Farm looking for Shelby, Ryan, and Raina.
Miraculously, the task force gets the job done. However, Roarke still comes out victorious. He uses the task force as an example. He praises them. Now, the country is even more united, and all the states are supporting Roarke's idea for a constitutional convention.