Due to the sudden disapperance of her S.H.I.E.L.D. colleagues and to the fact that S.H.I.E.L.D. was labeled as a terrorist organization, Agent Piper struck a deal with General Hale who led the investigation. They reclaimed the Kree Orb and took it to the St. Louis Aerospace Facility, where Piper would activate it from time to time, knowing that if her colleagues were to see the light beams emitted by the artifact, they would automatically come to investigate.
S.H.I.E.L.D. was indeed informed by Noah of the light beams indicating a possible communications with extraterrestrials. They headed to the St. Louis Aerospace Facility, having recognized the Kree Orb's signal on their way. They infiltrated the facility and made their way through the building, worrying about the fact that it seemed completely desert.
The S.H.I.E.L.D. team eventually found the laboratory where the Kree Orb had been taken, along with Piper. Piper pretended that she had come to the facility to investigate the light beams just like her colleagues. While Leo Fitz and Jemma Simmons studied the artifact, Piper explained what she had done after her colleagues seemingly vanished from Earth and that she had sent the facility's staff away when the Kree Orb activated itself.
However, it turned out to be a trap for S.H.I.E.L.D. Piper revealed that she had been arrested and that she had agreed to bring her colleagues to General Hale, although she was convinced that no harm would come to them. At this moment, a team of Sleeper Mechs led by Ruby Hale also arrived in the St. Louis Aerospace Facility.
A fight erupted between S.H.I.E.L.D. and the Sleeper Mechs. At first, S.H.I.E.L.D. got the situation under control, but Ruby then joined the fight and sliced off Yo-Yo Rodriguez's arms, forcing the S.H.I.E.L.D. team to leave the St. Louis Aerospace Facility and to retreat to the Lighthouse with Piper and the Kree Orb.