(CBS) When you cover a case in the legal system, you always know that there is a surface-level story and several other themes that typically run levels deep below the surface. You always know, in other words, that the public stories offered by the judge and the lawyers and the witnesses and the parties represent only a fragment of the "truth, the whole truth and nothing but the truth." The last best example of this paradigm is the case of John Walker Lindh, the American Taliban.

When federal prosecutors reached a plea deal with Lindh last July, they declared that they had done so in order to help conserve limited resources needed to fighter bigger battles in the legal war on terror. As the first layer of the story, that explanation made perfect sense, especially since it was clear that the government had no evidence that Lindh had been involved in any way in the brutal murder of CIA agent Johnny "Michael" Spann. The government deserves praise for parceling out its resources in a reasonable fashion, and turning the Lindh case into more of a witch-hunt would have been unbecoming.

The second layer of the story was a bit more complicated but no less publicized. It was clear, although the government never explicitly conceded so, that prosecutors were open to a deal with Lindh because of the brutal way in which he was treated by his military captors in Afghanistan and the spurious way in which federal law enforcement officials had observed Lindh's constitutional rights. It is no coincidence that the Lindh deal came about on the eve of a scheduled week-long hearing that was going to bring into the open the specifics of how Lindh was treated and by whom. Whether the government ultimately prevailed or not, that hearing would have been significantly embarrassing to the feds.

And now, nearly eight months later, comes another fascinating layer to the Lindh story. It is a layer that further clarifies why the Lindh case ended when and how it did. In addition to the external problems the Justice Department faced in court in the Lindh case, Jane Mayer in the last issue of the New Yorker magazine now has chronicled serious internal problems at Justice relating directly to the government's treatment of Lindh. These problems of law and ethics and even morality were only rumor or speculation while the Lindh case was pending. Now they appear to be fact.

They appear to be fact because Mayer has updated us on the sad story of Jesseyn Radack, a young, smart attorney who worked last year in the Professional Responsibility Advisory Office, an internal ethics unit within the Justice Department. Radack warned federal prosecutors before the FBI questioned Lindh in Afghanistan that the law did not permit the government to interview Lindh without his counsel present. According to Mayer, Radack inquired further into the matter after the FBI went ahead and interviewed Lindh anyway and was dumbfounded to learn that the Justice Department had completely ignored the position the PRAO had taken.

Had Radack's story ended there it might be easy to chalk it up as a typical experience a young lawyer endures while learning the ropes. But it didn't end there. Shortly after the experience, Mayer reports, Radack was slammed in a performance review (after getting a bonus the year before). Next, the story goes, Radack learned that the feds had turned over to Lindh's federal judge only a small portion of the e-mails she had written about the legality of the Lindh interrogation despite an obligation to turn all of them over. Then, Mayer reports, when Radack looked in the file for written versions of the e-mails, she discovered that almost all of them were missing. And, finally, Mayer says that it was only after Radack recovered those e-mails from computer back up and bugged her bosses to disclose them that they were turned over to U.S. District Judge T.S. Ellis, III. If there is another side to this story, and there usually is, the government hasn't yet shared it with us.

But we do know that some of those e-mails were leaked last June to Newsweek and now Radack is herself the subject of an investigation by the Justice Department. She has an attorney who is trying to ensure that she is protected under federal law as a "whistleblower." If Radack's account is true, I hope that investigators look at the circumstances behind the apparent destruction of relevant evidence as heartily as they look at the circumstances behind the leak of those e-mails. But, surely, this serious internal spat — which ultimately could result in criminal charges against law enforcement officials — helps create a little more context to the story of the rise and fall of the Lindh litigation.

And what does this new layer to the story tell me? If true, it tells me that even a government that already holds most of the trump cards in the legal war on terror isn't necessarily above stacking the deck even further from time to time in order to achieve the results it wants. This unsettling reality didn't necessarily result in an unjust end to the Lindh case. But it ought to concern all of us at a time when the rule of law is perhaps more important than ever.