All the flowers died because Barry got the bees to sue the humans over honey sales. The people had to pay a big settlement and since the bees were now well-off, they didn’t have to work anymore… thus the flowers no longer getting pollinated.
So the movie ends w/ Barry leading all of the bees into helping get the last living flowers in the country to Pasadena in time to pollinate and bring back to life all of the dead flowers - saving the Tournament of Roses parade.
I’m pretty sure it was the other way around- the only living flowers in the entire country were in the Tournament of Roses Parade, so they stole a float and then had to get them from Pasadena to New York in time to save the New York flowers. Barry and the florist lived in New York, after all.