The mission of the game is to successfully complete the entire story while collecting gold bricks. The events of the complete Saga span from the walkabout trade federation to the aforementioned negotiations of Naboo in the Star Wars prequels I - the threat of ghosts against the second Death Star above the attack of the rebels Endor in the return of the Jedi.

Just like in LEGO Star Wars 2: The Original Trilogy, the central world takes place in the Mos Eisley Tavern. cantina has doors that allow players to access chapters I-VI levels, bonus levels, bounty hunter missions and arcade games. cantina has a character customizer, a key feature of LEGO Star Wars II.

In the PC, Wii, PlayStation 3 and Xbox 360 versions of the game, there are 160 gold bricks to collect; 120 of them are used for the main levels. Each level has three. One is to complete the level in story mode, the second is to collect a certain number of studs/coins to achieve "true Jedi" status, and the third is by collecting 10 LEGO "minikit" cans hidden in the level. For iOS, there are a total of 200 gold bricks, with an additional brick for each level, and after completing the challenge mode, players must find 10 hidden blue Minikit within 20 minutes. iOS also offers 12 gold bricks by completing the arcade game in the lobby.

There are 20 gold bricks for completing the Bounty Hunter quest, which includes capturing key figures of the Old Republic and Jabba the Hutt's rebellion. There are also 6 gold bricks available for completing bonus missions (10 in iOS) and another 14 bricks available for purchase at the tavern (8 in iOS).

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 is a special unlockable level in LEGO Star Wars: The Video Game), and the original Mos Espa Pod Race and Gunship Cavalry levels).

Most story levels are the same as those in the respective original games. The game contains two previously abandoned levels: "Anakin's Flight" and "Bounty Hunter's Pursuit", which were once intended to appear in LEGO Star Wars: The Video Game, but were cut during development. "Anakin's Flight" is based on the robot-controlled ship battles seen in the Naboo space battles and the Phantom Menace. It was originally conceived as a rail shooter level, but was later changed to a free-roaming style used in almost all vehicle levels in the game. Bounty Hunter Pursuit is from Attack of the Clones. It was also made as a free-roaming level, but unlike Anakin's Flight, it was included in the second episode. (In LEGO Star Wars: The Video Game, Attack of the Clones only has five story levels, instead of the standard six levels per episode that all other episodes have.)