The Clone Wars affected not just the physical galaxy but the Force itself. The massive loss of life, the suffering of billions, and the corruption of institutions created disturbances that Force-sensitive beings across the galaxy could feel. Jedi found their connection to the Force strained by the constant need for combat reflexes rather than meditative contemplation.
The dark side grew stronger as the war progressed, though its source remained mysterious to the Jedi. The Sith plot orchestrated by Darth Sidious created ripples in the Force that clouded Jedi foresight, making their traditional role as galactic guardians increasingly difficult. This Force-clouding would prove crucial to the Sith plan, preventing the Jedi from discerning the true nature of the threat they faced.
Dooku's role as Darth Tyranus became known to the Jedi, confirming their suspicions that the Sith were behind the Separatist movement. However, they remained unaware that the Sith controlled both sides of the conflict, manipulating the entire galaxy toward an predetermined outcome.