The mission for the game is to successfully progress through the entire story while collecting Gold Bricks. The Complete Saga spans the events that take place from the Trade Federation negotiations above Naboo in Star Wars Episode I - The Phantom Menace to the Rebel attack on the second Death Star above Endor in Return of the Jedi.
Like in Lego Star Wars II: The Original Trilogy, the hub world takes place in the Mos Eisley Cantina. The Cantina has doors that allows the player to enter the levels for Episodes I-VI, the bonus levels, the Bounty Hunter missions, and the Arcade games. The Cantina features a character customizer, a key feature from Lego Star Wars II.
In all versions of the game except for the Nintendo DS version, there are 160 gold bricks to collect; 120 of these are for the main levels. There are three for each of the levels. One is for completing the level in story mode, the second is for achieving "True Jedi" status by collecting a certain amount of studs/coins, and the third is by collecting 10 LEGO "minikit" canisters, which are hidden across the level. For iOS, there are 200 Gold Bricks overall with an additional gold brick available for each level with the completion of a challenge mode where the player must find the 10 hidden blue Minikits in 20 minutes. The iOS version also offers 12 gold bricks by completing the arcade games in the lobby.
There are 20 gold bricks for completing the Bounty Hunter missions, which involve capturing key figures of the Old Republic and Rebellion for Jabba the Hutt. There are 6 further gold bricks for completing the bonus missions (10 in the iOS version) and another 14 available to purchase at the Cantina (8 in the iOS version).
Overall, there are 36 story levels, 20 bounty hunter missions, and 6 bonus levels (two Lego City levels, two story levels (Anakin's Flight and A New Hope, the latter of which was a special unlockable level found in Lego Star Wars: The Video Game), and the original Mos Espa Pod Race and Gunship Cavalry levels).
Most of the story levels are the same as those found in their respective original games. This game incorporates two previously scrapped levels: "Anakin's Flight" and "Bounty Hunter Pursuit," which at one time were intended to appear in Lego Star Wars: The Video Game but were cut during development. "Anakin's Flight" is based on the Naboo space battle against the droid control ship seen in The Phantom Menace. It was originally envisioned as a rail-shooter level, but was changed to the free-roam style used in almost all vehicles levels in the game. "Bounty Hunter Pursuit," focuses on Obi-Wan Kenobi and Anakin Skywalker pursuing bounty hunter Zam Wesell across Coruscant from Attack of the Clones. It was also made into a free-roam level, but unlike "Anakin's Flight" was incorporated into Episode II. (In Lego Star Wars: The Video Game, there were only five story levels for Attack of the Clones rather than the standard of six levels per episode for all other episodes.)
The "Mos Espa Podrace" and "Gunship Cavalry" story levels have been redesigned, although the versions from their respective original games are present as bonus levels. "Battle Over Coruscant," though, remains the same, with the change that players can change vehicles in Free Play. New additions to The Complete Saga include a 2-player Battle Arena mode called "Arcade Mode", new Minikit vehicle bonus missions, the red power bricks from Lego Star Wars II: The Original Trilogy returning and being incorporated into the prequel trilogy levels, and 10 additional bounty hunter missions add new challenges to the Prequel trilogy portions originally seen in Lego Star Wars: The Video Game.
The Episodes I, II, and III levels have been updated so that characters can build and ride vehicles, wear helmets and gain access to bounty hunter and Stormtrooper areas. Prequel trilogy characters now have the ability to dodge blaster fire and have their own special melee attack (for example, Chewbacca rips off arms). New Force moves were added, Force Lightning and Force Choke. New characters have also been added, bringing the total up to 128. Indiana Jones is an unlockable playable character to foreshadow and promote Lego Indiana Jones: The Original Adventures.