An issue of What If revolves around the Secret Invasion.^{[volume & issue needed]} The first story asks what would happen if the Skrulls won the Secret Invasion and eliminated poverty, war, famine, crime... and freedom. Here, the Skrulls are celebrating their anniversary of taking over Earth. Some of the humans have been converted into Skrulls. The Skrulls' problems is that the Avengers Alliance of Freedom (led by Captain America II and consisting of Black Panther, Blue Marvel, Human Torch, a heavily alcoholic Iron Man, Khn'nr, Ms. Marvel, Night Thrasher II, Spider-Man, Spider-Woman II, Storm, Thing, Thor, and Wolverine) are considered terrorists to the rest of the world. The Skrull's broadcast is interrupted by a pirate footage of Captain America stating that Earth is really under occupation. Queen Veranke's consort Norman Osborn tells her that it would be best to crush the Avengers Alliance of Freedom in Wakanda where they are currently hiding. Wolverine has brought one last remaining sample of the modified Legacy Virus to use against the Skrulls. He is the only survivor of the X-Men who were wiped out in San Francisco. Veranke appears before the United Nations getting an approval to invade Wakanda and take down the Avengers Alliance of Freedom. As soon as the virus was ready, the Skrull forces attack Wakanda. The Avengers leap into action to repel them. In the midst of the fighting, the cannon meant to release the vaccine is destroyed, so Thor uses his powers to spread across the globe. But instead of doing what was expected, every Skrull and converted humans perishes. The culprit is in fact Norman Osborn posing as Iron Man. He explains that this was all an elaborate ruse to get what he wants. Due to Iron Man's alcoholism, Spider-Man helped him infiltrate Wakanda to help them but he didn't expect that Norman Osborn would cross the line. Now, he can only lament what he has done. Norman Osborn admits that he did create a cure for the virus, so that he could survive and get back at the Skrulls for using him. In rage, Captain America beheads Norman Osborn with his shield. The Avengers surrender to the UN forces send to arrest them. Meanwhile far up on the Moon, Uatu can only lament how this alternate Earth turned out.

The second story asks what would happen if the Secret Invasion remained secret. Norman Osborn is shown wondering what would happen if he was in charge of national security. Already on this Earth, Captain America has been pardoned for his role in the Civil War and is seen shaking hands with the Red Skull. Hours later, Norman Osborn and the Thunderbolts are dispatched to investigate a situation in the Savage Land. They infiltrate a mysterious structure, discovering a vault full of duplicates of superhumans from outside. The Thunderbolts attempt to fight through, only for they all to be massacred and Norman Osborn captured. He is brought before Veranke/Spider-Woman, who talked to him as if she knew him. She tells him a little story about how a priest stood up to her and told her that she would die by the hands of Norman Osborn himself. Therefore, the Skrulls had to integrate themselves into human society and eventually fade away. She claims that the prophet became Osborn himself. Though Norman Osborn tries to deny it, Veranke insists that he is and asks that he kiss her true face. Instead, Norman Osborn commits suicide reverting him to his Skrull form. In truth, apparently said prophet has been cloned and placed with Norman Osborn's identity at which the Skrulls attempted deprogramming.