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Before the publication of the manifesto, Theodore Kaczynski's brother, David Kaczynski, was encouraged by his wife Linda to follow up on suspicions that Ted was the Unabomber. David Kaczynski was at first dismissive, but progressively began to take the likelihood more seriously after reading the manifesto a week after it was published in September 1995. David Kaczynski browsed through old family papers and found letters dating back to the 1970s written by Ted and sent to newspapers protesting the abuses of technology and which contained phrasing similar to what was found in the Unabomber Manifesto.

Prior to the publishing of the manifesto, the FBI held numerous press conferences requesting the help of the public in identifying the Unabomber. They were convinced that the bomber was from the Chicago area (where he began his bombings), had worked or had some connection in Salt Lake City, and by the 1990s was associated with the San Francisco Bay Area. This geographical information, as well as the wording in excerpts from the manifesto that were released prior to the entire manifesto being published, was what had persuaded David Kaczynski's wife, Linda, to urge her husband to read the manifesto.

After the manifesto was published, the FBI received over a thousand calls a day for months in response to the offer of a $1 million reward for information leading to the identity of the Unabomber. There were also large numbers of letters mailed to the UNABOM Task Force that purported to be from the Unabomber, and thousands of suspect leads were sifted through. While the FBI was occupied with new leads, David Kaczynski first hired private investigator Susan Swanson in Chicago to investigate Ted's activities discreetly. The Kaczynski brothers had become estranged in 1990, and David had not seen Ted for ten years. David later hired Washington, D.C. attorney Tony Bisceglie to organize evidence acquired by Swanson and make contact with the FBI, given the likely difficulty in attracting the FBI's attention. He wanted to protect his brother from the danger of an FBI raid, like Ruby Ridge or the Waco Siege, since he assumed Ted would not take kindly to being contacted by the FBI and would likely react irrationally or violently.

In early 1996, former FBI hostage negotiator and criminal profiler Clinton R. Van Zandt was contacted by an investigator working with Tony Bisceglie. Bisceglie asked Van Zandt to compare the manifesto to typewritten copies of handwritten letters David had received from his brother. Van Zandt's initial analysis determined that there was better than a 60 percent chance that the same person had written the letters as well as the manifesto, which had been in public circulation for half a year. Van Zandt's second analytical team determined an even higher likelihood that the letters and the manifesto were the product of the same author. He recommended that Bisceglie's client immediately contact the FBI.

In February 1996, Bisceglie provided a copy of the 1971 essay written by Ted Kaczynski to the FBI. At the UNABOM Task Force headquarters in San Francisco, Supervisory Special Agent Joel Moss immediately recognized similarities in the writings. Linguistic analysis determined that the author of the essay papers and the manifesto were almost certainly the same. When combined with facts gleaned from the bombings and Kaczynski’s life, that analysis provided the basis for a search warrant.

David Kaczynski had attempted to remain anonymous at the outset but he was swiftly identified, and within a few days, an FBI agent team was dispatched to interview David and his wife with their attorney in Washington, D.C. At this and subsequent meetings with the team, David provided letters written by his brother in their original envelopes, so the use of postmark dates enabled the enhancement of the timeline of Ted Kaczynski's activities being developed by the Task Force. David developed a respectful relationship with the primary Task Force behavioral analyst, Special Agent Kathleen M. Puckett, with whom he met many times in Washington, D.C., Texas, Chicago, and Schenectady, New York, over the nearly two months before the federal search warrant was served on Theodore Kaczynski's cabin.

David Kaczynski had once admired and emulated his older brother, but had later decided to leave the survivalist lifestyle behind. He had received assurances from the FBI that he would remain anonymous and that his brother would not learn who had turned him in, but his identity was leaked to CBS News in early April 1996. CBS anchorman Dan Rather called FBI director Louis Freeh, who requested 24 hours before CBS broke the story on the evening news. The FBI scrambled to finish the search warrant and have it issued by a federal judge in Montana; afterwards, an internal leak investigation was conducted by the FBI, but the source of the leak was never identified.

Paragraphs 204 and 205 of the FBI search and arrest warrant for Ted Kaczynski stated that "experts"—many of them academics consulted by the FBI—believed the manifesto had been written by "another individual, not Theodore Kaczynski". As stated in the affidavit, only a handful of people believed Theodore Kaczynski was the Unabomber before the search warrant revealed the cornucopia of evidence in Kaczynski's isolated cabin. The search warrant affidavit written by FBI Inspector Terry D. Turchie reflects this conflict, and is striking evidence of the opposition to Turchie and his small cadre of FBI agents that included Moss and Puckett—who were convinced Theodore Kaczynski was the Unabomber—from the rest of the UNABOM Task Force and the FBI in general:

204. Your affiant is aware that other individuals have conducted analyses of the UNABOM Manuscript __ determined that the Manuscript was written by another individual, not Kaczynski, who had also been a suspect in the investigation. 205. Numerous other opinions from experts have been provided as to the identity of the unabomb subject. None of those opinions named Theodore Kaczynski as a possible author.