Skyship Academy by Nick James

 The Pearl Wars (Skyship Academy #1)

A devastated Earth's last hope is found in Pearls: small, mysterious orbs that fall from space and are capable of supplying enough energy to power entire cities. Battling to control the Pearls are the Skyship dwellers—political dissidents who live in massive ships in the Earth's stratosphere—and the corrupt Surface government.

Jesse Fisher, a Skyship slacker, and Cassius Stevenson, a young Surface operative, cross paths when they both venture into forbidden territory in pursuit of Pearls. Their chance encounter triggers an unexpected reaction, endowing each boy with remarkable—and dangerous—abilities that their respective governments would stop at nothing to possess.

Enemies thrust together with a common goal, Jesse and Cassius make their way to the ruins of Seattle to uncover the truth about their new powers, the past they didn't know they shared, and a shocking secret about the Pearls.

Crimson Rising (Skyship Academy #2)

Our best-selling sci-fi series continues

Following their dramatic showdown in Seattle, Jesse Fisher and Cassius Stevenson find their world’s been turned inside out. The faculty at Skyship Academy is keeping Jesse a prisoner in his own home, fearful of his influence over Pearls. And Cassius, once a loyal Pearlhound for the Unified Party, has been pushed into hiding, fearful of his government's retaliation.

When Jesse smuggles a mysterious red Pearl onboard the Academy, he sets loose a destructive chain of events, which lead him to a reunion with Cassius and a confrontation with Theo -- a bloodthirsty Pearlhound with a dangerous secret.

But a larger threat looms in the stars. An enemy is gathering, with plans to exterminate the entire human race. And Jesse and Cassius might just be the lynch pins that trigger mankind's destruction.