The Hijacker is a device able to infect large systems with a virus that, in time, sequentially destroys all the sub-systems attached to it.
Sunil Bakshi handed a Hijacker to Agent 33 in order to neutralize the rest of S.H.I.E.L.D. agents while bringing Phil Coulson to a trap, having used a Photostatic Veil to mimic Melinda May's appearance. Agent 33 went to Bus, tricking Coulson into leaving with her to the Hotel La Ona placing the device on the plane to keep the rest of agents busy and ultimately to destroy the plane.
The device started to shut down the energy of the plane, destroying some of its systems, closing the cargo ramp and locking the emergency exits to trap the agents inside the plane. As Skye and Alphonso Mackenzie were first assessing the situation, Leo Fitz located the Hijacker, learning they had been sabotaged.
Knowing the device, as it was based on S.H.I.E.L.D. technology, Fitz tried to explain to the rest of agents that, if they did not stop the Hijacker, the plane would explode; a virus was liberated in the plane's systems and started to sequentially destroy the stabilizers, monitors, navigation systems and the communications before disrupting the wings, which would trigger an explosion big enough to destroy the whole plane, since the fuel was stored inside the wings.
Fitz took Lance Hunter to the avionics room of the plane, as he knew how to stop the virus but did not have the accuracy with his hands to properly do it. He needed to guide Hunter to do it for him, as the rest of agents were repairing the systems that had already fallen to delay the virus, and Hunter was the only one without technical skills to help with that. Fitz guided Hunter through the process, and, despite Fitz's troubles communicating, they successfully fixed the plane, with both agents celebrating the success.