The Shepherd Method is a treatment plan created by Meredith Grey and refined by Derek Shepherd to treat people with inoperable malignant gliomas, by injecting the tumor with a virus that would attack and shrink the tumor.
During the surgical contest, the residents receive patients from a bear attack, and Meredith is assigned to one of the lesser injured patients, however, he was the one who caused the bear to attack. Meredith looked for a further history and discovered he acted unusually, even for her. She ordered a CT scan which confirmed a brain tumor, an inoperable one. ("Where the Wild Things Are")
Meredith begins doing research and approached Derek with the work, despite the fact that they had recently broke up and he was dating Nurse Rose, however, he was the best there was. After he agreed to help, they started a clinical trial. ("Where the Wild Things Are")
During surgery they went in blind, effectively unsure of how the virus would work, hoping to find something but continually refining the virus mixture and changing its delivery. 12 of their patients died except for their last, Beth Monroe. ("Freedom, Part 2")
The treatment was published in a medical journal and named The Shepherd Method. Meredith was annoyed that it was called the Shepherd method (since she came up with it), but he insisted that she was only a baby yet and that he was the driving force behind it. After speaking with Bailey, he apologized to Meredith and used his pull as a "fancy neurosurgeon" to give her a kidney in a jar, much to the envy of the other residents.