As the time of the Great Flood draws near, Noah rounds up all the animals and instructs Donald to ensure that they all get onto the Ark. The animals refuse to get on at first, but after a bolt of lightning nearly hits them, they comply. While he is checking them off on his list, Donald realizes Daisy has not yet come aboard. He rushes back to their hut to get her, not seeing her get on as he does. Suddenly, a giant wave crashes over their hut, washing it away. Daisy, who is watching from the Ark's window, doesn't see Donald rush back to the ark in time and thinks he got washed away too. Similarly, Donald thinks the same thing about her as he failed to notice she wasn't still in the house and both are saddened by the apparent loss of one another.
A few days later, after the rain has let up, Donald sends out a male dove to check for land, angrily pulling him away from his mate whom he refuses to leave in the process. Upon seeing the female dove cry because her mate is gone, Donald realizes that he is missing Daisy more and more. Elsewhere on the Ark, Daisy looks at a picture of her and Donald that she keeps in a locket, and begins to feel the same way. Throughout the voyage, neither duck knows that the other is there.
When the ark lands, Donald looks on as the animals, some of which had young during the journey climb off. As Noah is leaving, he ruffles Donald's head feathers affectionately to congratulate him on a job well done, but Donald continues to feel sad about the loss of his girlfriend. Elsewhere, Daisy is walking down the plank when she realizes that her locket has fallen off its chain. Going back to look for it, she finds it and bends down to pick it up. Donald, having noticed the locket as he stepped out to sweep up some dirt, reaches down to pick it up at the same time. They both see one another and are overjoyed to see that the other is alive. Daisy kisses Donald and they walk away together to admire their new home under a beautiful rainbow.