Malware debuts in an alternate future, where he absorbs a time travel machine, and travels to the canon time. He doesn't appear in his yellow, incomplete form, but he appears in his other three main forms. He is killed by the end of the episode. He makes another appearance later in Dimension 10, Ben's dimension. He is revived by Gaia, and serves him. He is defeated easily.
He is revived later and attacks Galvan Prime by destroying Galvan B. Luckily, John was there at the time, and prevented a large scale attack.
Malware, in the Ben 10 dimension, is revived by the powers of Gaia. He serves him and attacks Ben, defeating him. Ben then takes on Gaia's power, destroying him.
In the time of Ben 10,000, Malware is revived, and upgraded, becoming Dalek-Malware. He serves Glacia, the main protagonist, and kills Samurai's mom, unlocking Samurai's powers. Samurai destroys him 10 years later.