Shinra Electric Company
mainly having Shinra's weapons/troops go against Zack to see how good they are
Monster Research Project
Midgar has a monster problem (yes, it was caused by Hojo's experiments escaping)... and Shinra needs to keep a lid on it somehow...
also keeping the monster population down in areas all over the world
Genesis's Forces
that army of Genesis Copies needs to be dealt with somehow
To End the War with Wutai
Wutai might have surrendered... but that didn't mean their army didn't stop being an issue
Hojo's Laboratory
Hojo needs to get combat data for his experiments somehow...
early ones include Summons (looks at how Summons are gotten in Remake)
a lot of these are implied to be happening while Hojo had Zack and Cloud after Nibelheim
Seeking Precious Items
people pay Zack to go Indian Jones around the world
people who employ him include... Midgar City Development Department, City Planning Dept. (don't ask me why there's two departments that sound so similar)
a lot of these are various Shinra departments sending Zack out to steal items from other compteteors the departments somehow have... including Don Corneo!
Seeking Priceless Items
more confirmation that stealing items from Shinra makes good money and that Shinra would really like their stolen items back!
Shinra has a lot of weird ways of finding items... including experiments in ESP and looking for rare item creators and recruiting them
Zack, the Materia Hunter
starts out as Shinra sending Zack out to find materia since they can somehow scan for it remotely
by the middile it turns out Yuffie has somehow getting Zack's (and Shinra's) emails and is getting them to send Zack to retrieve materia for her
by the end, Yuffie is going out to dangerous locations and Zack is being sent out after her just in case she gets into trouble... and because her item info is always good
Great Cavern of Wonders
Shinra is exploring the caves up in the Northern Crater... too bad they're in a race against the Genesis army and Wutai to find whatever is hidden there and Shinra's mecha keep malfunctioning the further in they go... and Hojo released some monsters down there...
is the location of the optional super-boss, Minerva... yes, the boss form of the thing Genesis sees....
Mysteries of the World
Shinra would really like to give Zack a proper vacation, but it keeps getting interrupted by all the monsters that keep attacking Costa del Sol