On Oct. 8, we published an investigation examining how a judicial opinion in a pivotal lawsuit brought by a Guantanamo detainee vanished, only to be replaced weeks later by an entirely different opinion. At the center of our reporting are two documents representing separate versions of that same opinion: the original opinion written by Judge Henry H. Kennedy, and a second opinion quietly put in the original's place more than a month later.

Why are there two opinions? As reporter Dafna Linzer explains, redactions that were supposed to be made in the original opinion never were. Once government security officials, who are responsible for reviewing and redacting classified information from sensitive cases, discovered the error, the decision was quickly removed from the court file. In Judge Kennedy’s courtroom four days later, the Justice Department refused to have the opinion redacted and re-released. With the detainee, Uthman Abdul Rahim Mohammed Uthman, slated for indefinite detention, the stakes were high. Officials did not want to risk that those who had seen the original opinion would know exactly what the government had meant to keep classified.

The opinions have one striking similarity -- neither contains the vast redactions characteristic of documents relating to habeas cases -- and an equally significant difference -- the second opinion is eight pages shorter than the original.

We used DocumentCloud to note what’s different about the two documents. We started with the second opinion, the one now available to the public, and annotated every place it differs from the original.

For each change, we added a public note.

Inside each note, we restored the words that had been deleted or altered from the original opinion in bold text, allowing readers to compare both sections of the two opinions at once.

To provide context for the reader, we labeled each note as a deletion or change, and added a short description. For instance, in the screen grab below, the second opinion left out that Pakistani authorities had seized Uthman so we titled the note: “Deletion: Who seized Uthman and when.” Because the titles of notes also appear in the right-hand sidebar of the document, readers can see all the changes at a glance, and easily explore the document.

The original opinion had 10 more footnotes than the second, which explains the many annotations on footnotes being referenced and renumbered. Judge Kennedy’s signature is also missing from the second opinion. For more on what changed, check out our table of the most interesting deletions.

We're not the first news organization to use DocumentCloud as a way to explore a source document. Back in April, the news applications desk at The Chicago Tribune discovered a computer glitch that made redactions in former Illinois Gov. Rod Blagojevich’s motion to subpoena President Obama visible. They used DocumentCloud to reveal each redaction. The Arizona Republic annotated the state’s controversial Senate immigration bill after Judge Susan Bolton’s ruling stopped several sections from going into effect. Other great examples can be found on the DocumentCloud site.