Bobbi Morse was commissioned by S.H.I.E.L.D. director Phil Coulson to discover the latest schemes of the terrorist organization HYDRA, but the position she earned as head of security at the HYDRA Laboratories did not allow her to access information about HYDRA's projects.Jemma Simmons was assigned by Coulson to infiltrate HYDRA Laboratories. Simmons was not told of Morse's assignment or Morse's supervisory role in her mission. Daniel Whitehall learned that Raina stole the Obelisk  and threatened her to have it brought to him. She went to Calvin Zabo to retrieve it, but he dismissed her, telling her to beg Whitehall for her life. Going to HYDRA Laboratories, Raina saw Simmons in communication with S.H.I.E.L.D.
Raina attempted to blackmail Coulson into getting the Obelisk for her by threatening that she would reveal Simmons as a spy. Coulson, knowing he had a backup plan, allowed Raina to send her text message to HYDRA.
EscapeJemma Simmons had her cover blown due to Raina sending an email to every HYDRA operative at the HYDRA Laboratories, with a photo of Simmons using the Flex Screen that incriminated Kenneth Turgeon. Sunil Bakshi ordered his men to grab Simmons, but she escaped the room, coming across Bobbi Morse, head of security at the Laboratories. Simmons thought she was done, but Morse attacked her escort, revealing her identity as a fellow undercover S.H.I.E.L.D. agent. Morse instructed Simmons to wait while she got rid of some guards, but Simmons witnessed Bakshi approaching her position. Both Simmons and Morse ran to the roof where, following a brief shootout between Morse and the HYDRA operatives pursuing them, both agents jumped off the roof onto a cloaked Quinjet piloted by Antoine Triplett.
Bobbi Morse and Jemma Simmons rejoin S.H.I.E.L.D.. Simmons had an awkward reunion with Leo Fitz after leaving him months earlier. Morse is reunited with her ex-husband Lance Hunter, much to his dismay.
Morse stole Simmons' hard drive from the HYDRA Laboratories which would later help S.H.I.E.L.D. to learn about Vincent Beckers and his connections to the Red Skull and the Splinter Bombs used during the Attack on the United Nations.Morse's cover within HYDRA was blown; a video file of her fighting HYDRA operatives was sent to Toshiro Mori during the Infiltration into Toshiro Mori's Estate. Realizing the facility had been compromised by S.H.I.E.L.D., Daniel Whitehall ordered all operations to be dismantled and moved to a new location. As he watched his office being packed-up, Whitehall was approached by Calvin Zabo who presented him with the Obelisk and offered to show Whitehall how to use it. When asked why he would do that, Zabo stated that together he and Whitehall could kill their mutual enemy, Phil Coulson.