Unlike Saints Row and Saints Row 2, which had three separate story arcs for each gang with a prologue and epilogue, missions in Saints Row: The Third have multiple interwined storylines. 3 Count Beat Down - unlocks 3 Count crib.Stop all the Downloading - unlocks Burns Hill Reactors crib.Pimps Up, Hos Down - unlocks Safeword crib.Hit the Powder Room - does not unlock Powder as a crib.Stronghold missions count for an extra 2% towards 100% Completion, in addition to being counted as one of the 47 missions in the game. Strongholds are part of the main arc and unlock special Cribs. In Saints Row: The Third, taking over neighborhoods is accomplished through City Takeover. In Saints Row and Saints Row 2, Strongholds are special missions which unlock neighborhoods and do not contain storyline antagonists, but are required to be completed before the finale of each gang's arc. Excluding these, and counting Gangstas in Space, there are 25 missions in the game.

This count includes 14 compulsory activities, 4 cutscenes, 4 strongholds, and both instances of Three Way. The Statistics and the Save/Load Menus state that there are 47 missions in Saints Row: The Third.

Respect, a form of currency that is needed to start missions in Saints Row and Saints Row 2, is not needed to play missions in Saints Row: The Third, but is instead used for Upgrades. Each leads to its own respective bonuses. Some missions require the player to make decisive choices.

Missions are essentially levels which allow progress through the storyline of Saints Row: The Third.

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