Following Captain America's exposure of HYDRA's secret existence within S.H.I.E.L.D., a signal was sent to all HYDRA agents to start the HYDRA Uprising. S.H.I.E.L.D. facilities everywhere were in chaos, including the S.H.I.E.L.D. Academy, the Cube, and the Triskelion, as HYDRA agents attempted a coup.
Hand, thinking that Coulson was a traitor, diverted the Bus to the Hub and sent two S.H.I.E.L.D. UAV's to destroy John Garrett's S.H.I.E.L.D. Jump Jet. Garrett was able to destroy the UAV's with the help of Coulson and board the Bus.
The Bus landed at the Hub and Victoria Hand ordered her agents to use portable Overkill Devices to disable the Bus. Melinda May attempted to contact Nick Fury but was informed he was dead before being shot in the arm through the window. Phil Coulson patched her wound and Skye downloaded all the data onto a hard drive before wiping the Bus' computers.
Before Hand's agents stormed the Bus, Leo Fitz used the Mouse Hole to get the team and John Garrett out of the plane. They then divided into two groups; Skye and Grant Ward went to disable the Hub's computers while the others searched for Jemma Simmons and Antoine Triplett. Garrett dressed as a low level agent and pretended to bring in Coulson, Fitz, and May as captives. Agent Baylin, on security duty, was then knocked unconscious by Garrett as the others were incapacitated by Coulson's team.
As Garrett gave reasons why Hand should be killed, he mentioned that Raina and Coulson were both subjected to the Theta Brain-Wave Frequency Machine by the Clairvoyant. This fact was never revealed by Coulson, causing him to realize that John Garrett was the Clairvoyant. Garrett confirmed it as guards surrounded them.
Coulson ordered the guards to arrest Garrett, but Garrett told those recruited by Jasper Sitwell to do their job, causing the undercover HYDRA guards to kill the loyalists. Garrett then offered Fitz a place among HYDRA and Coulson and May death. Before the guards could execute their orders, Skye and Ward blew the computer, causing the lights to go out and giving Coulson's team the advantage. A battle then ensued where the guards were subdued by May and Fitz, and Garrett was knocked out by Coulson with the Thunderstick.
Victoria Hand, accompanied by her loyalists, stormed the room. She knew that Garrett was a traitor because of bugs planted in the room. Garrett and his agents were arrested.
With the destruction of the Triskelion, the Hub became one of S.H.I.E.L.D.'s main headquarters. Victoria Hand left Coulson in charge as he was the highest ranking uncompromised officer and chose to go to the Fridge with the prisoner, John Garrett. Grant Ward opted to go also, but he, as a HYDRA sleeper, killed Hand and released Garrett.