Preface: If you question the FBI’s anthrax investigation, but don’t want to read anything questioning the government’s 9/11 investigation, please read this  first.
There are numerous parallels between the anthrax and 9/11 investigations. This essay will touch on a couple of them.
1. Continuously-Changing Story When Caught in Misstatements
The government has continuously changed it story each time it has been caught in a misstatement in both the anthrax and 9/11 investigations.
When it was pointed out that the FBI’s timeline made no sense, they simply changed it  without explanation.And the government initially claimed that Iraq was behind the attack . When the Iraqi connection was disproven, the government tried to blame it on Mark Hatfill. After Hatfill won a multi-million dollar judgment against the FBI for defamation, they had to change their tune yet again.
“In April, it was reported that the FBI had been focusing on as many as four suspects. Fox News identified them as a “former deputy commander,” presumably in the U.S. Army, a “leading anthrax scientist,” and “a microbiologist.” The fourth suspect was given no description. Now the bureau is “confident that Dr. Ivins was the only person responsible for these attacks,” according to the assurances of the U.S. Attorney for the District of Columbia.” 
And yet, after Ivins’ death, the FBI is now trying to pin it solely on the dead guy.
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The military put out 3 entirely different stories about what happened on 9/11. Specifically, Norad was forced to give 3 entirely different versions of what happened that day , as each previous version was exposed as false, or as providing evidence that the government could in fact have intercepted the hijacked planes had they followed standard protocols.
The Senior Counsel to the 9/11 Commission, who led the 9/11 staff’s inquiry, said “I was shocked at how different the truth was from the way it was described …. The tapes told a radically different story from what had been told to us and the public for two years…. This is not spin. This is not true.” 
2. Pre-Ordained Conclusions
In regards to both anthrax and 9/11, the government decided on a politically-acceptable explanation, discounted any other possibilities, and then made arguments to support the acceptable conclusion.
The government’s pre-ordained conclusion is that only one person was involved in the anthrax attacks. However, leading experts say  that it would have taken more than one person to produce the advanced, weaponized anthrax.
Moreover, as mentioned above, the initial pre-ordained conclusion was that Iraq was responsible. Moreover, as mentioned above, the initial pre-ordained conclusion was that Iraq was responsible. Specifically, the FBI was actually instructed to blame the Anthrax attacks on Al Qaeda by White House officials .
Once the alleged Iraqi connection became impossible to maintain (and once the false connection had already succeeded in helping to provide a justification for launching the Iraq war), the blame switched to a single rogue U.S. scientist (Hatfill), and then – once Dr. Ivins died – to the conclusion that Ivins was the culprit, as that would provide a tidy ending to the story. In fact, as shown below, the FBI had not been convinced that Ivins was the culprit even a few months before his death.
The Joint Congressional Inquiry was only authorized to look at “intelligence failures”, and nothing else. The pre-ordained conclusion, therefore, is that intelligence failures were the sole cause of the 9/11 attacks, a politically acceptable conclusion.
The 9/11 Commission could only publish a report which was approved by the White House. Moreover, the Commission specifically said that “it is not our purpose to assign blame ” for the attacks. It necessarily follows that if blame could not be assigned, then the only possible conclusion could be that “no one could have foreseen” 9/11.
As shown elsewhere, other agencies tasked with investigating other aspects of 9/11 were tasked with supporting the pre-ordained conclusions of the official account.
3. Failure to Follow Leads
In both cases, the government failed to follow any leads which contradicted the pre-ordained conclusion.
The FBI apparently failed to conduct investigations at the most likely points of origin: Dugway, Battelle, or the numerous other labs which had the strain .
The FBI also failed to follow up on investigating a letter sent before the attacks which may very well have pointed to the culprit .
Because a Bush White House insider  was executive director of the 9/11 Commission, and determined which issues and lines of evidence would be considered, many relevant lines of inquiry were not followed.
The government allowed members of the Saudi royal family, including the Bin Ladens, to leave the country  right after 9/11, without meaningful interrogation.
4. Suppression of Evidence
The government suppressed evidence in both cases.
The FBI kept Congress in the dark about the investigation for many years. Until recently, “the FBI has completely shut Congress out of its … investigation into anthrax attacks on Capitol Hill and around the nation” .
The FBI has also failed to share with the public even details of its investigation which could not conceivably threaten national security.
Investigators for the Congressional Joint Inquiry discovered that  an FBI informant had hosted and rented a room to two hijackers in 2000 and that, when the Inquiry sought to interview the informant, the FBI refused outright, and then hid him in an unknown location, and that a high-level FBI official stated these blocking maneuvers were undertaken under orders from the White House.
The official investigators into the collapse of the World Trade Centers were denied access to the site and the evidence contained there, or even access to such basic information as the blueprints for the world trade center .
The government claims that no flight recorders were recovered from the airplanes which hit the Twin Towers. However, firefighters stated they did recover the flight recorders . And Dan Rather confirmed  that they were recovered.
The 9-11 widows who pressured the administration to create the 9/11 Commission have declared it a failure which ignored 70% of their detailed questions and “suppressed important evidence and whistleblower testimony that challenged the  official story on many fronts“ .
5. Destruction of Evidence
The government allowed important evidence to be destroyed in both cases.
The FBI allowed 70 years of Ames-related anthrax samples to be destroyed. As noted in the San Francisco Chronicle :
“Scientists in and out of government say the rush to destroy the spores may have eliminated crucial evidence about the anthrax in the letters sent to Congress and the media.”
As a top bioweapons expert and insider to the FBI investigation said :
“This was an astonishing thing to do. It should have been preserved as evidence. This was a roadmap of everybody and anybody that had gotten access to develop the super-strain that hit Leahy and Daschle.”
Moreover, according to the Associated Press :
“FBI scientists early on had — but destroyed — the unique strain of anthrax used in the deadly 2001 attacks that years later would lead them to Dr. Bruce Ivins…:
[This was anthrax that] Ivins took from his Army lab in February 2002 and gave investigators”
The FBI’s excuse for destroying the anthrax sample which Ivins gave them makes no sense .
The government filmed the interrogations at Guantanamo of 9/11 suspects, who – according to the 9/11 Commission – were the key basis for the Commission’s findings – but hid the existence of the tapes, and then destroyed the tapes  before any outside observers could watch them.
The tape of interviews of air traffic controllers on-duty on 9/11 was intentionally destroyed by crushing the cassette by hand, cutting the tape into little pieces, and then dropping the pieces in different trash cans around the building as shown by this NY Times article (summary version is free; full version is pay-per-view)  and by this article from the Chicago Sun-Times .
And the government hauled away and then promptly shipped overseas virtually all of the steel from ground zero before it could be analyzed by scientists. Indeed, the former head of the fire science and engineering division of the agency now investigating the world trade center disaster, who is a professor of fire protection engineering, wrote that evidence necessary to determine the cause of the collapse of the World Trade Centers was being destroyed .
6. Allegations of Bribery
The government apparently attempted to bribe people to support its story in both cases.
If the FBI attempted to bribe Ivins’ own son, it is logical to assume that they attempted to bribe other people (perhaps successfully).
According to a Pulitzer-prize winning reporter, the U.S. paid $5 million to an Iraqi for his assistance in letting the CIA forge and backdate a letter falsely linking 9/11 to Iraq .
7. Skeptical Congressmen
Congress people who have examined the evidence are skeptical about the government’s explanation in both cases.
Congress people from both sides of the aisle question the government’s version of 9/11 .
8. Skeptical Experts
Experts who have examined the evidence are also skeptical about both cases.
Many top anthrax experts are skeptical that Ivins could have done it by himself  (and see this ).
Top scientists , engineers, arthitects , high-level intelligence officials , military leaders  and others with relevant expertise  are skeptical of the government’s explanation of 9/11.
The foregoing list just begins to document the many parallels between the anthrax and 9/11 investigations. I started with a list of 14 major parallels but – for the sake of brevity – reduced it to 8. There are many other parallels which could be written about. Writers should take up the task of listing additional parallels.
Even for the parallels mentioned, the list is in no way intended to be exhaustive. Again, for the sake of readability, I solely gave a couple of examples for each parallel, when entire essays could (and hopefully will) be written about each one.