In the opening sequence, Yuffie is seen with Vincent aiding in the evacuation of Midgar just before Meteorfall (retconning their absence in the final FMV of the original game).
She rescues Vincent from the top of the Sister Ray just before it collapses.
Later in the game, Zack will receive e-mails from the "Treasure Princess" luring him into side missions for treasure.
In each mission, Yuffie will make an appearance to steal the treasure.
On the date with Yuffie, she makes advances towards him and even plants a kiss, but Cloud denies any interest.
(Interestingly enough, Yuffie is the only character that gets to kiss Cloud on the date.) Yuffie first appears in this game when Zack raids Fort Tamblin.
She also provides a lot of energy and humor to otherwise serious situations.
In the closing sequence, Yuffie is at 7th Heaven, asking Tifa if they've heard anything from Cloud concerning Vincent’s whereabouts.Yuffie shows up later to aid in the battle against Bahamut SIN (after recovering from her motion sickness).