On the surface, Mohamed et al v. Jeppesen Dataplan, Inc. was about whether or not the government could invoke the states-secrets doctrine in order to dismiss an entire case on the grounds that it would expose government secrets and harm national security. The state-secrets doctrine, prior to the last administration, had typically been used to block specific pieces of evidence from being used -- not entire cases from being heard. The Obama administration has continued the Bush-era expansion of the state-secrets doctrine.
The Jeppesen case was really about accountability for torture. The five plaintiffs in the case said they had been rendered to third countries where they were tortured as part of the Bush administration's extraordinary rendition program. They were suing the private companies that the government had contracted to help facilitate transportation. By refusing to take this case, the Supreme Court let stand a previous 9th Circuit ruling in favor of the government. Decisions to hear a case only require four votes -- which means at least one of the four Democratic nominees to the court joined their conservative colleagues to prevent this case from being heard.
What this means is that if the government sends you to be tortured in a foreign country you have no recourse against the private company that facilitated your torture as long as the government declares it a state secret. As I wrote last year, this means that "you can't sue the government, you can't sue the private company that was involved, and frankly you can probably count on the people who helped facilitated it getting good jobs elsewhere in the same field." In the absence of any kind of decision from the courts indicating that the Bush administration's actions were illegal, the only thing standing in the way of torture being used again is a flimsy, reversible executive order that could be withdrawn the day the next Republican president is inaugurated.
There is awesome, limitless power for the government in secrecy. As long as it keeps matters under wraps, the courts have decided for themselves that they will not check the power of the executive branch, meaning that when the president does it, it's not illegal as long as he can keep it a secret. This should help put the Obama administration's aggressive pursuit of whistle-blowers into greater context -- virtually the only avenue left for accountability when the government breaks the law is through exposure in the press.
UPDATE: Justice Elena Kagan recused herself, which would have denied the moderate wing of the court enough votes on its own. I said something like this could happen, if not in this case specifically.