Despite his inexperience (and a few missteps), Fitz showed quick thinking, ingenuity and courage during the assignment and was essential to the successful completion of the mission. Fitz watched helplessly with the rest of the team as Phil Coulson was captured by Raina and the Centipede Project. Sometime later, Fitz and Agent Grant Ward were assigned by Agent Victoria Hand to infiltrate the border of South Ossetia and destroy an enemy weapon known as the "Overkill Device". He became irritated as the team laughed at his misfortune, and he demanded to know who was responsible, completely unaware of Melinda May's guilt in the prank. While on the team, Fitz became good friends with teammates Grant Ward and Skye. Slowly regaining his skills, Fitz was able to get back into doing active field and lab work, and played an important role in the conflicts with Robert Gonzales' S. Fitz and Simmons were able to locate the Bus, and Coulson ordered them to leave the area immediately.

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Fitz and Jemma Simmons traveled to the Stati Corp company to gather information concerning the tragic accident that had occurred there. Gill briefly thanked Fitz and Simmons for saving him, and apologized for ruining their speech. On Ward's suggestion, Fitz visited Gill in his dorm, and the two instantly connected.

Relenting in his comfort, Simmons spoke with her parents on the phone, a task she had been procrastinating. Coulson's Team received a report of a mysterious attack at the S. Upon Fitz's orders, the machine was smashed, and the student, later revealed to be Donnie Gill, was saved.

He was caught in an explosion with Coulson and Ghost Rider by Eli Morrow and was almost sent into another dimension, but managed to get out. Simmons told him distressing news over the phone, that everything was not as it seemed, and Fitz rushed back to Gill's dorm. UAVs chasing Garrett as it became assumed that Victoria Hand was the Clairvoyant.

Fitz bid goodbye to Gill and began to head to the Boiler Room of the Academy at Simmons' request.

Simmons scanned the imprint of the staff in the tree where it was previously embedded, while Fitz worked to create a replica back in the lab. In the lab, Fitz designed a new weapon using Night-Night Gun technology, which he called the Night-Night Bracelet. The incident involved an indoor pool instantly being frozen, with young cadets in it.

In Trillemarka National Park, Fitz assisted Simmons in creating a 3D model of the recently discovered fragment of the Berserker Staff. In any and all assistance he could provide, he and Simmons hid supplies for Skye in a paper lunch sack, including a SAT phone for her to reach them.

The team located the source, along with Gill and Dormer, and brought them on board the Bus, seeing as Dormer was injured. Fitz watched Phil Coulson and John Garrett battle the S. During the Battle at the Hub, Fitz hid but his contributions saved his teammates' lives when it was needed.

Fitz was removed from the situation, and received news that Gill's weather machine had gone haywire, causing a massive storm. While Phil Coulson, May, Skye, and Fitz had a four-way argument about secrets, Victoria Hand redirected the Bus to kill Coulson's Team. Garrett offered Fitz a place in HYDRA while Fitz swore vengeance.

Although Simmons returned, Fitz was devastated to learn she had met and bonded with the astronaut Will Daniels. Also, Phil Coulson ordered the research must stay in house. Looking for a skillet to help Simmons make pancakes, Fitz found a message left by Skye, "Ward is HYDRA," just as Simmons found Agent Eric Koenig's body.

D.'s help, he went through a portal to a distant planet and rescued her. He and Simmons continuously monitored Skye and took blood samples in hopes of duplicating the miracle drug, but the Bus did not have equipment sufficient enough for the job. He told Skye about this just as it was realized that the Clairvoyant was a S. Fitz helped Coulson research their whereabouts, but he questioned Coulson's leadership after their experiences in Portland.

They escaped, but Fitz spent a long period of time without oxygen, causing brain damage. Fitz begged Ward to let Garrett die, telling him that he did not have to follow Garrett. As they were being escorted away by guards, Fitz and Simmons managed to escape their guards, but Ward found them, resulting in a chase. When Simmons woke up, he explained the situation to her: there was no way out of the container, and they were going to die. agents took the Bus to Florida because Phil Coulson wanted a painting that had the Words of Creation inscribed on its back.