|For the ambush of the Lighthouse by the Confederacy, see Siege of the Lighthouse|
|For the ambush of the Lighthouse by the Sibyl-Bots, see Attack on the Lighthouse|
After Leo Fitz and Jemma Simmons escaped from the Chronicoms with the help of Enoch, Malachi decided to enter their minds in the Cerebral Fusion Machine to help them. After gaining the knowledge of the escapees, Atarah wanted to use it to Time Travel, like S.H.I.E.L.D. did, to save Chronyca-2. However, Malachi opposed this idea, and wanted to reform on another planet and call it Chronyca-3. This being against Atarah's plans, Malachi executed her, and proceeded to take charge of the Chronicoms, reassigning them all to be Chronicom Hunters. When Enoch met up with Isaiah, the two fought, as Enoch was wanted by the Chronicoms. However, Enoch prevailed and stole Isaiah's skin to disguise himself as he grouped up with the Hunters. The Chronicoms then decided to use Earth as their new home, so they used Fitz and Simmons' knowledge to help them prepare an ambush.
The Chronicom Hunters all infiltrated the Lighthouse using the Inter-Planetary Conveyance Disc. They then proceeded to knockout all of S.H.I.E.L.D.'s equipment. After witnessing the apparent death of Melinda May, Leo Fitz and Jemma Simmons noticed that the comms suddenly went offline and they were mysteriously locked out of the system, followed by the satellites going offline too. The Hunters then bursted into the control room, opening fire on everyone, with no intention of taking prisoners. They successfully took control, although some agents were able to get away.
Going under emergency protocols, Trevor Khan's STRIKE team made their way to an unused floor, but they were discovered by the Hunters who know of it due to the knowledge they acquired from Simmons. They then lined up the agents and executed them. Fitz and Simmons soon discovered the bodies, causing them to wonder how the Hunters could have known about the protocols. When the realized they had accessed their minds, Fitz ordered Diaz to escort the remaining agents to Deke Shaw's development lab, as they only became aware of it recently. Meanwhile, the Chronicoms began retrieving multiple S.H.I.E.L.D. technology, including the Theta Brain-Wave Frequency Machine.
Knowing they had become a liability, Fitz and Simmons stayed behind and decided to use explosives to destroy all the data stored in the Lighthouse. They made their way to where the data was stored, seeing the Framework was kept there too, which made them realize the Hunters could use it to gain the knowledge of anyone who went in there, mainly Phil Coulson. They then begun to plant the explosives, soon realizing that they did not have a timer to set off the explosives. Simmons then grabbed a grenade, and both understood that they had to sacrifice themselves to prevent the Hunters from succeeding.
When a group of Hunters entered the room, Fitz and Simmons hid and prepared themselves to pull the pin, blowing up the room and the Hunters present. However, when they were spotted, causing them to pull the pin, two shots were fired, killing the Hunters. The shots were revealed to be from Enoch, who revealed he had taken Isaiah's skin, as he put the pin back in the grenade. Enoch the informed them that there were more Hunters coming, which Simmons knew they wouldn't be able to fight off. Enoch then began to propose a strategy to save their lives, for which they had to act quickly. Enoch then expressed that it would be the hardest thing that have done: changing the natural course of their lives forever, something that they were familiar with many times.
Leo Fitz, Jemma Simmons, and Enoch spent years developing time travel, and created a Life-Model Decoy of Phil Coulson. and then went back in time to 2019, where Simmons and Enoch saved the agents of S.H.I.E.L.D. from the Temple of the Forgotten. While Fitz waiting in a Containment Module, the agents boarded Zephyr One and traveled back in time to 1931, planning to stop the Chronicoms from undoing S.H.I.E.L.D.'s formation in history. They prevented Luke, Cain, and Abel from killing Freddy Malick and then followed the Chronicoms to the 1950s to prevent the Chronicoms from activating Project Helius and killing Daniel Sousa. Coulson managed to destroy the Chronicom's time ship, but the Chronicom's predictor, Sibyl, saved herself by uploading herself into the River's End power grid and partnering with Nathaniel Malick to attack Afterlife. Malick recruited a team to attack S.H.I.E.L.D.. The Chronicoms and Malick's team destroyed S.H.I.E.L.D.'s facilities, leading S.H.I.E.L.D. to regroup with the remaining agents of the S.H.I.E.L.D. of the 1980s, where Simmons constructed a Quantum Tunnel to bring Fitz to the 1980s. S.H.I.E.L.D. then returned to their timeline's 2019 and brought the Chronicoms and Malick's team with them. With help from Kora, S.H.I.E.L.D. gave the Chronicoms empathy, ending the Chronicoms' invasion before they could fully conquer the Lighthouse.
- Agents of S.H.I.E.L.D.: 5.22: The End
- Agents of S.H.I.E.L.D.: 6.01: Missing Pieces
- Agents of S.H.I.E.L.D.: 6.13: New Life
- Agents of S.H.I.E.L.D.: 7.13: What We're Fighting For
- Agents of S.H.I.E.L.D.: 7.02: Know Your Onions
- Agents of S.H.I.E.L.D.: Alien Commies from the Future!
- Agents of S.H.I.E.L.D.: 7.04: Out of the Past
- Agents of S.H.I.E.L.D.: 7.06: Adapt or Die
- Agents of S.H.I.E.L.D.: 7.07: The Totally Excellent Adventures of Mack and the D
- Agents of S.H.I.E.L.D.: 7.09: After, Before
- Agents of S.H.I.E.L.D.: 7.10: Stolen
- Agents of S.H.I.E.L.D.: 7.11: Brand New Day
- Agents of S.H.I.E.L.D.: 7.12: The End is at Hand