In Marvel's Avengers Earth Mightiest Heroes, the Skrulls lived in Skrullos until Galactus devoured their planet. This was part of a prophecy that also involved the Earth as saying that the Skrulls should proclaim Earth for themselves (but this was not true). As the Kree set their sights on Earth, then the Skrulls began infiltrating in all major organizations including S.H.I.E.L.D. and the Avengers.
Having replaced Captain America, for two months they tried to get information from him, but no success. In some of these attempts, Captain America manages to escape. Rogers interrogates the Skrull Interrogator. While Rogers sneaks inside the ship he meets Madame Viper, both of them join forces to return to Earth. Later, the two meet; an A.I.M. scientist named Lyle Getz, two S.H.I.E.L.D. agents named Clay Quartermain and Mockingbird, the Invisible Woman from the Fantastic Four, a member of the Serpent Society King Cobra and the director of S.W.O.R.D. Henry Gyrich.
Seeing as his prisoners escaped, the Commander sends the Super Skrull to stop them. Later, the Commander sends all troops of the the ship to make sure they do not escape. Eventually, the prisoners manage to escape. The Commander notifies this to the Queen Skrull, but she was not disappointed since they already knew how to subdue the humans.
Ms. Marvel followed a Skrull ship to Wakanda, when that ship opens, she sees the "Avengers". They tell her the story how they were captured by the Skrulls (which was false). They tricked Carol. The Skrull Avengers fight against Black Panther and his troops. Eventually the real Avengers arrive at Wakanda to fight the Skrulls. After being defeated, Iron Man (Skrull) say this is just the beginning. Meanwhile, Queen Veranke captured Black Widow, Iron Man, Nick Fury and Quake.
After the Queen gave the order to begin the invasion, every Skrull infiltrated and destroyed the defenses from each organization that was infiltrated. Veranke tells Tony that thanks to him they could defeat the Avengers. Meanwhile the other Avengers fought against the Skrulls. Later, Captain America (Skrull) gives a message to Earth to surrender and take over the Earth by wiping out most of the human race. Eventually, the Skrulls have been defeated and arrested for their crimes.
They appeared in Marvel's Avengers Assemble as a cameo in the crowd of Mojo's battle arena. One of the main enemies of The Fantastic Four, the Skrulls captured earthlings and replace them with Skrull imposters.
In Hulk and the Agents of S.M.A.S.H. as part of the concurring force. They took the form of humans in a mall which turned out to be a Skrull spaceship.