The Skrulls made their first appearance in Fantastic Four #2 (Jan. 1962)
Millions of years ago, the Celestials performed genetic experiments on the reptilian ancestors of the Skrulls, resulting in three branches of Skrulls that eventually warred with one another. The Deviant branch — possessing the innate ability to shapeshift — were triumphant, and afterward wiped out all members of the other two races until only two were left: the Skrull Eternal, Kly'bn and Prime Skrull of the original Skrull race. Kly'bn implored them to spare his life, as killing him would kill part of their heritage. The Deviants' leader, Sl'gur't, fell in love with him, with the two eventually becoming the gods of the Skrull pantheon. As Kly'bn could not change, Sl'gurt vowed to never keep the same shape for too long. Prime Skrull escaped to Earth in the 20th Century and later became a member of the Underground Legion. From that point, the Skrulls began to expand their territory. The Deviant branch later split into two more groups, the modern Skrulls and an anomaly called the Dire Wraiths, a parasitic race that could still shapeshift and had use of magic, but were not as technologically advanced as the Skrulls.
The modern Skrulls originate from the planet of Skrullos, and were originally a mercantile civilization, primarily interested in free trade and willing to share their technology with all races they deemed worthy. When they encountered a new race, they simply transformed themselves to resemble that race. The Skrull empire that resulted from these contacts was based on free trade and mutual cooperation. The empire is controlled by an Emperor and each of the 978 worlds is controlled by a Governor.
Eventually, the Skrulls developed long-distance space travel; a great tour of the universe was undertaken, led by Emperor Dorrek, and in a full decade of travel no civilization was encountered he deemed superior to the Skrulls. Finally, the Skrull delegation reached the planet Hala, home to the then-barbaric Kree and the peaceful Cotati, and held a contest to determine which of the races would represent Hala to the Skrull Empire. Seventeen members of each race were taken to different uninhabited planetoids where they were left with sufficient supplies for one year. At the end of that period, whichever group had done the most with themselves would be adjudged the most worthy. The Kree were taken to Earth's Moon where they built a great city while the Cotati were taken to another barren world in a different solar system and used their abilities to create a beautiful park. Realizing that the Cotati were going to win, the enraged Kree killed all the Cotati. When the Kree revealed that they had solved the question of who would represent Hala to the Skrulls by destroying their opposition, the Skrull delegates were appalled and vowed that Hala would forever be banned from their circle of favored worlds so the Kree massacred them as well, took over the Skrull landing spaceship by force, and developed their own technology from it.
Because of the immense distances involved, decades passed before the Skrulls learned of the Kree’s activities. By this time it was too late. The Kree were now advanced and audacious enough to attack the Skrulls in their home galaxy. During the millennia that followed, the Kree aggression forced the Skrulls to become a militaristic civilization, and the Skrulls eventually developed the vicious streak needed to conduct intergalactic war. Their entire culture was remade in the warrior image. The Kree-Skrull War continued for thousands of years with only brief interruptions. The Skrull Throneworld is later moved from Skrullos to the more central Tarnax IV, with their empire encompassing over fifty worlds. The Skrulls also created the first Cosmic Cube, which later became the Shaper of Worlds; the Shaper related that, upon attaining self-awareness, he lashed out blindly, destroying two thirds of the Skrull empire and casting the civilization back into barbarism (suggesting this occurred before the war with the Kree broke out).
The Kree Accuser Ronan had wrested control of the Kree Empire from the Supreme Intelligence and attacked the Skrulls, reigniting hostilities. The Avengers become involved once the Super Skrull kidnaps Captain Marvel, and in turn they battle a Kree Sentry robot, three of the original Skrulls that had fought the Fantastic Four, S.H.I.E.L.D. agents, rogue Inhumans and legions of Skrulls. The Supreme Intelligence ends the immediate conflict by revealing to Avengers' ally Rick Jones that he has vast mental potential, which is then used to freeze all combatants in place. The Supreme Intelligence announces that, while the Kree and Skrulls have reached genetic dead ends, the human race displays incredible untapped potential. It was revealed years later that the conflict produced a Kree-Skrull hybrid, Hulkling, who is the child of one-time lovers Captain Marvel and the Skrull Princess Anelle.
Second Kree-Skrull War
Later Reed Richards discovered that yet another Governor-turned-Emperor, Zabyk, had created a genetics bomb, which, when it exploded made all the Skrulls lose their shape-shifting abilities. Whatever form they were in they were stuck in at the time of the explosion.
In desperation, since without their shapeshifting powers they were vulnerable, they managed to kidnap the herald of Galactus, Nova, in an attempt to get Galactus to destroy Kree worlds for them. Their plot failed when the Silver Surfer helped Galactus rescue Nova in exchange for his freedom from Earth.
When the Celestials made an appearance, this scared the Skrulls into starting a second war with the Kree to show they were not powerless. The attack was first made by Kylor, one of five governors claiming to be Emperor. He had a spy in the Kree Empire, Nenora, who gave him the early edge. They tried to hide their secret weakness at all costs from the Kree.
Kylor was eventually betrayed by Nenora, as was the entire Skrull race. She assumed power of the empire and wished to keep it for herself. It was Empress S'byll who stepped up to control the Skrulls and finish the war. She was able to resurrect the Super Skrull and he returned to find the empire in shambles. They tricked the Silver Surfer into attacking a Badoon fleet, which he was not aware were allied with the Kree. Since the Kree waged war on the Surfer, he allied himself with the Skrulls to save Zenn-La from destruction.
To restore their powers, the Super Skrulls DNA needed to be transferred to S'byll, because only a female could spread the ability to the other Skrulls. The Surfer helped them to power a machine that would return the Empress' shape shifting abilities. The device was successful. With this power she was able to restore every Skrull she touched and became the true Empress of the Skrulls.
She and Super Skrull waged war with the Kree with the help of the Silver Surfer. She replaced Super Skrull with Captain Reptyl and he helped to change her into an emotionless reptile. But Reptyl was betrayed by one of his own and the Skrull fleet was utterly destroyed by the Kree. S'byll and Silver Surfer went alone to attack the Kree homeworld of Hala.
Gaining the knowledge that Nenora was actually a Skrull gave them the advantage. S'byll gave her shape-shifting abilities back to her, crippling her and showing the Kree her true self. A peace treaty was created.
The Skrulls eventually broke that peace treaty as they kept their military drive and prefer to fight rather than negotiate. Among the other races contained within the Skrull Empire are the Druff, Guna, Kallusina, Morani, Pheragot, Queega, Tekton, and Yirbek races. Other races remain independent, whether through treaties or open resistance. Such races include the Clegrimites, Gegku, Krylorians, Wilameanis, and Xandarians. The Skrull-Xandarian war with the Xandarians recently ended with the destruction of Xandar by the supervillainess Nebula.