The Second Sith theory was a marginalized theory held by some members of the Jedi Order during the Separatist Crisis and later the Clone Wars. Not officially endorsed by the Jedi High Council as being a legitimate belief, the theory postulated that the Zabrak dervish that killed Jedi Master Qui-Gon Jinn had been a Sith Lord. If this were true, then those who believed that the Rule of Two had been maintained among any possible Sith survivors suggested there must be a second Sith: either a master or an apprentice. The theory was further advanced by Count Dooku's conversation with Obi-Wan Kenobi, where he implicated one Darth Sidious in manipulating the Galactic Senate.
The theory of the so-called "Second Sith" originated in 32 BBY when reports out of the Theed Royal Palace were received at the Coruscant Jedi Temple. Jedi Master Qui-Gon Jinn had been cut down by the same Zabrak dervish that had ambushed him on Tatooine. The Zabrak, garbed in black and wielding a double-bladed lightsaber in the style of Sith Lord Exar Kun, was well-versed in the ways of the Force and was able to draw upon the dark side for strength.
While the assassin had been killed by Jinn's Padawan, Obi-Wan Kenobi, rumors spread when investigations showed that members of Queen Padmé Amidala's Advisory Council had overheard Trade Federation Viceroy Nute Gunray refer to the Zabrak as "Darth Maul". Swearing the Queen and her council to secrecy and asking them not to spread information about the Sith, the Jedi set the debacle to rest. While Jedi High Council member Mace Windu privately questioned the idea of a second Sith hiding in the shadows during Qui-Gon's funeral, neither he nor Grand Master Yoda could determine the truth beyond speculating whether or not Maul was an apprentice of the master.
Over the following decade, talk of the return of the Sith remained a topic of private conversation within the Jedi Temple, just as word spread of the suspicions that Anakin Skywalker would come to fulfill the ancient Prophecy of the Chosen One. With the name "Darth Maul" impossible to corroborate, there seemed to be no other leads. Despite such fanatics as Granta Omega cropping up during the turbulent time of the Separatist Crisis, the High Council refused to speculate on the matter and counseled patience and meditation in the matter.
With the lack of evidence providing little relief to those frustrated with the identity of Darth Maul, scant trace accounts of the Rule of Two kept the mystery alive. Some Jedi began to suspect that the a Sith may have avoid death during the Seventh Battle of Ruusan and gone into exile. Others, however, dismissed the notion out-of-hand. Council member Ki-Adi-Mundi was adamant in his belief that the idea was obscene, declaring that the Sith had been extinct for a millennium and the Order would have detected their return. When accusations arose and pointed to Count Dooku as being a Sith, Mundi proclaimed him to be a political idealist rather then a Sith.
The theory was revived when Dooku himself revealed to an imprisoned Kenobi on Geonosis that a Sith Lord named Darth Sidious was secretly in control of the Galactic Republic. This control, Dooku alleged, came through Sidious' manipulation of thousands of Senators who unwittingly served the Sith agenda. Dooku went on to claim that Viceroy Gunray had served Sidious at Naboo, but had been betrayed and abandoned by the Sith when he no longer served a useful purpose. During the ensuing battle and the showdown between Dooku and Grand Master Yoda, Dooku's actions revealed that he was indeed in league with the Sith but did not answer the fundamental question of whether or not he was the master or the apprentice. Rumor spread quickly at the Jedi Temple of the possibility of a Second Sith being involved in Republic politics. Most Jedi continued to dismiss this as too far-fetched to even consider: the Jedi would be aware of a Sith takeover within the Galactic Senate. Many Jedi, including Kenobi, believed that Dooku was using this as a deception to cover up his own fall to the dark side and to paint himself in a stronger light.
Despite this, several marginalized Jedi dissented from the status quo. Jedi Master Quinlan Vos went undercover on behalf of Master Tholme in hopes of corroborating the existence of the Second Sith. Vos went so far undercover that hunting the elusive Sith became his obsession and his only claim to his former identity. Dooku understood this and sent Vos on a wild bantha chase across Coruscant, convincing Vos that Senator Viento was actually a Sith Lord. Infiltrating Viento's apartment, Vos did battle with his fellow Jedi Master K'Kruhk and nearly killed him, as he assassinated the Senator. Realizing he had been deceived, Vos eventually returned to the Order proper, but still harbored his belief that Dooku was simply the apprentice. Jedi Gokim Keeg was another dissenting member of the Order, believing that Dooku's claims were not a ruse and actually held some truth to them.
By the height of the Clone Wars, most of the Jedi High Council began to fear that the Sith had actually penetrated the Republic Military's highest echelons as several coincidences and discrepancies were made apparent. Mace Windu in particular became concerned with those surrounding the Supreme Chancellor himself, believing that he was but a puppet of the Sith. Windu's suspicion fell on Senate Vice Chair Mas Amedda.
It wasn't until Master Kenobi recovered the mechno-chair of Viceroy Gunray that the High Council could definitively link Dooku with some mysterious, shadowy figure. Two members of the Council were convinced that Dooku was in fact the master, having been self-taught by a Sith holocron he uncovered or ancient lore found on Korriban. As more evidence presented itself in the final weeks of the war, Yoda revealed the hunt for the Second Sith to Supreme Chancellor Palaptine and informed him of an ongoing investigation in the Works district of Coruscant. The Jedi had tracked the Sith to an abandoned building there and believed that the Sith was using it as a base.