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 the Earth for them. 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 without success. In some of these attempts, Captain America manages to escape. Rogers interrogates the Skrull Interrogator. While Rogers is sneaking inside the ship he meets Viper, then the both of them join forces to return to Earth. Later, the two meet with more prisoners like King Cobra, Mockingbird, Invisible Woman, etc.
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.
Miss 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 Skrull. But all this was a farce to trick Carol. The Avengers Skrull fight against Black Panther and his troops. Eventually the real Avengers arrive at Wakanda to fight the Skrull. After being defeated, Iron Man (Skrull) say this is just the beginning. Meanwhile, Queen Veranke captured Fury and Iron Man.
After the Queen gave the order to begin the invasion, every Skrull infiltrated 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 before the Skrull. Eventually, the Skrull are defeated and banished from Earth.
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 impostors.
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.