The Marvel series followed a more vulnerable Fury as he returned to Earth decades after promising to find the Skrulls a home.
A certain Skrull, Gravik, was particularly hurt by his broken promises, leading a rebel group in the hopes of causing war on Earth and wiping out the human race.
So, as Fury finally confronts Gravik, here's everything you need to know about how Secret Invasion ends.
Secret Invasion ending explained: What happened to Gravik?
The episode begins with Fury going to confront Gravik at the heart of New Skrullos. Elsewhere, Rhodey (Don Cheadle) - who's still a Skrull in disguise - attempts to get President Ritson (Dermot Mulroney) to take action against the Russians, who he claims are hiding the Skrulls, after the attack on the motorcade.
Fury discovers New Skrullos littered with bodies and begins to weaken due to his exposure to radiation within the compound. He finally confronts Gravik, who taunts him in his weakened state. He tells Fury that the skin he's chosen was the first person he ever killed, who Fury told him to kill during his first mission, and insists that the violence wreaked upon Earth is Fury's fault.
Fury admits he failed Gravik, and knew within a few years of searching that the only option was to build the Skrulls a home on Earth - but changing the humans' minds would be too difficult. Fury offers Gravik exactly what he wants: The Harvest - samples of the Avengers' DNA - in return for leaving Earth alone. Gravik refuses.
As Fury and Gravik are enveloped in the Super Skrull machine, an enhanced Gravik goes to punch Fury - but Fury catches his fist and, with his own enhanced powers, throws Gravik through the wall and across the compound. As Fury approaches Gravik, it's revealed that, all this time, he has been G'iah (Emilia Clarke) in disguise.
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She's ready to wreak revenge on him for killing her parents and, in an epic fight, the pair of them embody some of our favourite MCU heroes' powers, including the Hulk (Mark Ruffalo), Groot (Vin Diesel), Mantis (Pom Klementieff) and, of course, Captain Marvel (Brie Larson). After an airborne battle, G'iah puts Gravik to sleep and he plummets to the ground, with G'iah eventually defeating Gravik.
What happened to Rhodey?
Elsewhere, Sonya Falsworth calls Skrull Rhodey, urging him to move the President from his current room in the hospital, as Fury has "lost it" and is on his way. Rhodey takes action, moving the president, as the Secret Service are taken out one-by-one by silenced gunshots.
The assailant is revealed as Falsworth, who knows Rhodey's a Skrull. Plus, it turns out the real Fury is with Falsworth in the hospital. As he approaches the President, he urges him to believe that Rhodey is a Skrull, revealing to the President that various world officials have been kidnapped by the Skrulls and the real humans are in pods below the Skrull compound - and that if nukes the compound, he nukes the innocent people.
As the President grapples with what to believe, Skrull Rhodey breaks free from Falsworth's grip - but Fury is ready and shoots him in the head, revealing once and for all that he is a Skrull. The president immediately makes a call to halt the nuclear strike.
After G'iah defeats Gravik, she rushes down to where the pods are, freeing all of the humans who had been used as skins for the Skrulls - including the real Rhodey, who's wearing a hospital gown. Heartbreakingly, fans noticed there's something wrong with Rhodey's legs - which seems to suggest he's been a Skrull since Captain America: Civil War and might not know his friend Tony Stark (Robert Downey Jr) is dead. Everett Ross (Martin Freeman) is also freed.
Although the President makes his statement to the world, he uses it to declare war on the Skrulls, prompting attacks on Skrulls and innocent humans alike.
What happened to G'iah and Falsworth?
After her battle with Gravik, G'iah is ambushed by Falsworth. Falsworth urges G'iah to work with her as leader of the Skrulls.
She says that their deal will be different to Fury's with Talos (Ben Mendelsohn), and that together they'll make the planet safe for both of their people.
What happened to Fury?
Fury then heads home to see his wife Priscilla/Varra (Charlayne Woodard). He tells her she knows where she can find him if she can forgive him.
He encourages the president to act now to stop the war between the humans and Skrulls, but Ritson says the only way to help the Skrulls is to get them away from Earth.
The final scenes of the episode show Fury leaving Earth once again after reuniting with Varra in her own skin and telling her that the Kree are open to peace talks. Varra decides to stay on Earth, but leaves things on a good note with Fury as he departs.
Secret Invasion is available to stream now on Disney Plus. Sign up to Disney Plus for £7.99 per month or £79.90 for a full year’s subscription.