The "flower" was an organism from the immense spacecraft Rama that the cosmonaut Jimmy Pak discovered in a fenced enclosure. It heavily resembled a plant with blue feathery leaves and a cluster of three flowers with dozens of green, blue and violet petals. "Plucking" the flower caused it to retreat into the ground, which Jimmy believed to have killed it.
Whatever the actual consequences of that event, it was most certainly killed by the ship's preparation for leaving the Sol system and the years it would spend in the cold interstellar void.