The movie begins and ends with a quote from Andrew Marvell's poem "The Garden" - "The mind, that ocean where each kind Does straight its own resemblance find; Yet it creates, transcending these, Far other worlds, and other seas".
In the end, Dr. Haber does cure Orr. This is represented by his jellyfish, representing normality, now swimming with a large school of jellyfish. Also, in the final scene, Manny, who has always taken care of Orr throughout all the changes, does not recognize him.
The movie has two love stories, George Orr and Heather Lelache and also Dr. Haber and Penny. After Orr says you can't dream someone away if you love them, Haber and Penny are seen. Later, after Haber changes everything, he and Penny are still together now as doctor and patient.