Extraordinary Measures, based on events in the life of John Crowley and his family, dramatizes the father's quest to find a cure for Pompe disease, a relatively rare genetic condition that afflicts two of his three children.  The quest brings into play three powerful, often competing human motives:  a father's love for his children, a scientist's pursuit of knowledge and recognition, and a corporation's mandate for profits.  Crowley (Brendan Fraser), an energetic marketing executive, and his wife Aileen (Keri Russell) are told that their children Megan (Meredith Droeger), age eight, and Patrick (Diego Velazquez), age six, have reached the upper limits of their life expectancies.

When Megan, an affectionate, playful, and clear-sighted child, is rushed to the hospital with symptomatic heart and respiratory failure, a young physician empathically encourages the parents to think of their only daughter's immanent death as a "blessing" that will end her suffering.  However, Megan survives.  "So I guess you could say we dodged that blessing," Crowley echoes back to the doctor.  Seeing Megan's will to live reinforces John's wish to make her well, and he abruptly abandons his promising career to find a medical researcher who can reverse Pompe's effects. 

Immersing himself in medical journals and websites, John discovers the intriguing research of Robert Stonehill (Harrison Ford).  A cranky, renegade scientist who thinks to the beat of rock music blasting from a boom box, Stonehill has developed a cutting-edge theory about correcting the enzyme deficiency in the cells of people with Pompe, which gradually weakens skeletal, respiratory, and heart muscles.  However, to produce a treatment derived from his theory, he needs more funding.  John immediately creates a fund to support Pompe research, and he and Stonehill form a mutually exasperating partnership.  They lock horns with each other, venture capitalists, and finally a large genomic research corporation, Zymagen.

Despite the scientist's abrasive ways, Zymagen gives Stonehill a lab and creates employment for Crowley.  However, the two confront the company's culture of rigorous competition among its scientists and its focus on profit margins that ignore the fates of individual children.  When the Zymagen scientists develop a promising therapy, they decide to offer the treatment only to infants, who are most likely to experience benefits.  Disqualifying Crowley's children from the promising trials, this decision, combined with Crowley's obvious conflict of interest, creates the film's final obstacle.  Stonehill and the executives uncharacteristically collaborate to overcome it. 

This ending might seem implausibly neat, but it's consistent with the film's mostly evenhanded approach to the dilemmas of pursuing treatments for orphan diseases.  Toward the end, we witness even Crowley, albeit uncomfortably, reaching beyond his fatherly motives for the Pompe project and turning his argument for bringing the treatment to market from children to profits.  The longer the patients live, John assures the executives, the more treatments Zymagen will sell.  The film leaves space for viewers to ask to what extent Crowley's argument creates a fair compromise or opens an ethical quandary.  In a closing narration, the film moves beyond the fictionalized characters and plot to the real Crowley children and a tempered victory.  Yes, the Pompe treatment stopped the progression of the disease and improved Megan's and Patrick's hearts.  But it has not cured the Crowley children, and almost certainly it won't.   The treatments do, however, show more success when taken at the onset of symptoms.