Over the course of four seasons, Star Wars Rebels told the story of the early days of the Rebellion. Its focus was on the crew of the Ghost, a Rebel cell known as the Spectres who were initially based on the Outer Rim planet of Lothal. They were quite successful at their jobs, which inevitably led to the Emperor sending increasingly dangerous agents after them. But some of the worst disappeared suddenly with little or no explanation.
The main recurring antagonist over the first two seasons was Agent Alexsandr Kallus of the Imperial Security Bureau. He was tasked with finding and stopping Lothal's Rebel cell. Over time other Imperials joined in on the action, including Wilhuff Tarkin, Darth Vader, Grand Admiral Thrawn and, eventually, even the Emperor himself. By the time Season 3 rolled around, however, Kallus had betrayed the Empire and was working with the Rebels.
In addition to Kallus, Kanan Jarrus and Ezra Bridger ran afoul of the Grand Inquisitor in Season 1. Formerly a Jedi Temple Guard during the era of the Republic, he now answered to Darth Vader in the Empire's ongoing purge of the Jedi. His mission was to find Force-sensitive beings and then either convert them to the Dark Side or kill them. As such, he was dispatched by Vader to deal with Kanan and Ezra.
The Grand Inquisitor also headed up a group of Force-sensitive agents loyal to the Dark Side called the Inquisitorius. This cadre of Inquisitors roamed the galaxy on similar missions to suppress any rebirth of the Jedi Order. After the death of The Grand Inquisitor at the end Season 1, the Seventh Sister and Fifth Brother hounded the Spectres. Eventually, the Spectres also ran afoul of the Eighth Brother.
Ezra, Kanan and Ahsoka Tano went on a mission to Malachor to find a way to permanently deal with the Dark Side and the Inquisitors. The Seventh Sister and Fifth Brother followed them there, while the Eighth Brother was already on Malachor, hunting Maul. In the end, Ahsoka and Kanan teamed with Maul to defeat the Inquisitors. Then, Darth Vader showed up and everything went sideways.
While the Inquisitors were used with some frequency in comics as well as the critically acclaimed game Star Wars Jedi: Fallen Order, Rebels was their only film or TV appearance. The deaths of the Eighth Brother, Seventh Sister and Fifth Brother marked the end of their run on the animated series, and they were replaced by Grand Admiral Thrawn. More than that, the Inquisitors essentially disappeared from the Star Wars universe as a whole.
Such a dominant and destructive group vanishing so completely was strange to say the least. As of the year 0 BBY, the Jedi were considered all but extinct by the Empire. Although this was obviously not the case as both Obi-Wan Kenobi and Yoda were still alive, as were Luke and Leia Skywalker, the core mission of the Inquisitorius to exterminate the Jedi Order may have been believed to be complete, meaning the Empire theoretically had no need for them anymore.
None of that explains where the Inquisitorius went or what happened to them, though. Four Inquisitors were killed during the course of Rebels, three of them in one episode. But they certainly were not the only Inquisitors in the galaxy. The question of the ultimate fate of their order deserves deeper exploration. They may have simply moved on to filling other roles within the Empire, though it's more likely Darth Vader "retired" them the same way he did the Jedi.
All four seasons of Star Wars Rebels are also available on Disney+.