In the movie Man of Steel, General Zod and his followers were sentenced to "300 cycles of somatic reconditioning" (not sure if I got that right). What exactly is somatic reconditioning and what does it do to a Kryptonian?
Answer
Short Answer
SPECULATION: Since Man of Steel's Kryptonians are genetically engineered for their occupations in life, warrior, scientist, scholar, statesman and presumably others, each lifestyle is assumed to have an ideal state upon birth of what each person is supposed to embody. This technology is supposedly well developed and highly respected for its results.
"Somatic Reconditioning" is a process by which the genetically engineered and bred Kryptonians reapply whatever process defines their occupational development to the cellular structure of the Kryptonian in order to remove deviant or undesirable behavior. As a social measure, it is likely a tool of last resort, since it likely causes permanent and irrevocable change in the person subjected to it. (Better than execution, but just barely.)
Longer Answer
There is likely no canon explanation possible for this statement. That said, I would like to offer a supposition based on the culture of the Kryptonians from Man of Steel and a bit that we do know about Kryptonians in general. It'll be quick.
We know that the Man of Steel Kryptonians were all genetically engineered, literally created from a matrix of desirable genetic combinations and were bred to their duties. Zod was a warrior and protector, and Jor-El was a scientist and scholar.
The matrix of genetic information which Jor-El entangles with Kal-El's DNA is the information for every Kryptonian there ever was, and now ever could be. Kryptonians (with the exception of Kal-El) were all born in an artificial birthing matrix. Presumably there are other such birthing technologies scattered through former colonies of Krypton.
Since the Council considered the followers of Zod, dissidents, perhaps the cultural method of dealing with deviation from the genetic programming one is born with, is to perform "somatic reconditioning" where the process used in the Kryptonian's birth is reapplied to correct for "environmental deviation" (or contamination). This would explain the term completely as somatic means dealing with the body and reconditioning implies some form of adjustment.
Such "somatic reconditioning" might act as a form of mental restructuring or dare I say, brainwashing, removing tendencies that might be considered deviant for a society which prizes order and structure above all other things. Since the Kryptonians did not believe in the death penalty (they created the Phantom Zone technology, after all) perhaps "somatic reconditioning" was their method of rehabilitation during a criminal's stay in the Zone.
This makes sense in light of the idea the Phantom Zone villains were bound in some unknown material before the strange sarcophagi were sent to the ship that would confine them to the Phantom Zone (presumably for 300 years).

The Phantom Zone villains encased in an unknown material before transporting them into their prison ship. It is this material, which we see them surrounded in right before they are transported that I speculate the "somatic reconditioning" will take place.
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