Aaron Swartz at a Boston Wiki meetup in 2009. (Photo: Sage Ross)

Programmer, writer and open-information activist Aaron Swartz was arraigned today in Middlesex Superior Court in Woburn for what authorities are calling computer intrusion, fraud and data theft — trying to provide unpaid access to the contents of Jstor, a not-for-profit archive of scientific journals and academic work.

He was released by Middlesex Superior Court Clerk Magistrate Michael Sullivan on personal recognizance with the condition that he surrenders his passport.

The official charges against Swartz, 25, once a fellow at the Harvard Ethics Center Lab studying institutional corruption, are breaking and entering with intent to commit a felony; larceny over $250; and unauthorized access to a computer network, Middlesex District Attorney Gerry Leone said. The charges result from the way he accessed Jstor on Sept. 24 and Oct. 9 and “continued to make over 2 million illegal downloads in November and December of 2010,” Leone said.

There are various questions muddying the case against Swartz, including whether the offended parties — Jstor and the Massachusetts Institute of Technology — are actually all that offended. The questions arose even as the federal indictment against Swartz was unsealed July 19.

The institute no longer has an ax to grind with Swartz, according to David Segal, executive director of Demand Progress, a liberal group for which Swartz once served as executive director.

“The alleged victim has settled any claims against Aaron, explained they’ve suffered no loss or damage, and asked the government not to prosecute,” Segal said at the time on the Demand Progress website, referring to the university.

A simultaneous statement by Jstor said the journal noticed Swartz’s attempts to download, “stopped this downloading activity, and the individual responsible, Mr. Swartz, was identified. We secured from Mr. Swartz the content that was taken, and received confirmation that the content was not and would not be used, copied, transferred, or distributed.”

The government’s case as of Wednesday sounded different. According to a press release from Leone’s office:

On Jan. 4, a newly installed security camera captured Swartz entering the restricted server room, appearing to replace a hard drive. On Jan. 6, the camera again captured Swartz entering the room, covering his face with a helmet in an apparent effort to evade identification. He is alleged on that date to have taken the concealed laptop and hard drive out of the room. Later that day, MIT police recognized Swartz from the video. When police called to him, he fled; police eventually apprehended and arrested the defendant on Lee Street in Cambridge. Upon his apprehension, Swartz was found to be in possession of a portable USB drive that contained a file-grabbing program designed to evade security measures and initiate mass downloads. When the laptop was examined forensically, it also contained a similar file-grabbing program that had been specifically designed to steal files from the JSTOR database.  Secret Service agents later seized four additional hard drives that contained the stolen files.

Swartz’ next court date is Jan. 3 for a pretrial conference.

Past coverage of the case is here.