Poindexter was convicted on multiple felony counts on April 7, 1990 for conspiracy, obstruction of justice, lying to Congress, defrauding the government, and the alteration and destruction of evidence pertaining to the Iran-Contra Affair. The conviction was overturned in 1991 on the grounds that he had been granted immunity from prosecution as a result of his testimony before Congress.
On February 13, 2002, the media learned that Poindexter had become the Director of The Pentagon's Information Awareness Office, a secretive intelligence bureau whose mission is to gather and centralize as much information as possible about everyone, intending to unify all private databases about U.S. citizens into one central database run by the government (including information about travel, credit card purchases, medical history, etc.). Controversy over Poindexter's integrity followed his appointment to the position due to his role in the Iran-Contra scandal.
In protest against what he feels is Poindexter's plan to effect the systematic destruction of Americans' civil liberties and privacy rights, San Francisco Weekly columnist Matt Smith published John Poindexter's home address and phone number on November 27, 2002, along with the names and addresses of his next door neighbors. The meme quickly propagated through the Internet, and Poindexter's phone number was disconnected shortly thereafter.
From 1961 - 1964 Poindexter was a laboratory assistant at the California Institute of Technology, where he conducted laboratory research to further develop a model for understanding the Mossbauer Effect with Nobel Laureate Rudolph Mossbauer.
Poindexter has served the White House as Military Assistant from 1981 - 1983, as Deputy National Security Advisor from 1983 - 1985, and as National Security Advisor from 1985 - 1986. Joining President Reagan's White House staff in 1981, from 1983 to 1985 Poindexter was responsible for leading and managing the National Security Council Staff and was Chairman of the Crisis Pre-planning Group. As National Security Advisor, Vice Admiral Poindexter was responsible for providing recommendations to The President on national security, foreign policy and defense policy. Major events in which he played a significant role included: Strategic Defense Initiative, Operation Urgent Fury, Achille Lauro incident, Libyan Operation to respond to terrorist attacks, the Reykjavik Summit with Soviets, peaceful transition of government in the Philippines, and the Iran-Contra Affair.
From 1988 to 1989 Poindexter was senior scientist at Presearch, Inc Presearch had primarily been involved with defense studies and analysis. Faced with anticipated defense budget reductions, Poindexter joined the firm to develop new commercial enterprises. He designed and developed hardware and software for the prototype of a digital real-time, imaging system to be used for physical security of high value facilities. It was used to obtain a contract for a nuclear power plant security system.
From 1990 to 1996, Poindexter served as co-founder of TP Systems, Inc TP Systems was a software development firm specializing in commercial software for the IBM PCs and compatibles; Poindexter was the chief designer and programmer. Development included a symbolic debugger for multi-tasking environments, a BBS communications program, and numerous utility programs.
From 1993 to 1996, Poindexter served as a consultant to Elkins Group. Elkins was a business alliance with Electronic Data Systems (EDS), which has developed the Elkins Interactive Training Network (EITN), a satellite based training delivery system. Poindexter was the Chairman of the Maritime Advisory Committee and a member of the Board of Directors. He also provided advice on strategic planning.
From 1996 to 2002 Poindexter served as Senior Vice President for SYNTEK Technologiex. SYNTEK is a small high technology firm with contracts in domestic and international defense and commercial business. Poindexter was responsible for high-level advice on management and direction of information systems projects (for example Defense Advanced Research Project Agency's Project Genoa).
As of December 2002, Poindexter serves as the Director of DARPA Information Awareness Office (IAO). The mission of the IAO is to imagine, develop, apply, integrate, demonstrate and transition information technologies, components, and prototype closed-loop information systems that will counter asymmetric threats (most notably, terrorist threats) by achieving total information awareness: enabling preemption; national security warning; and, national security decision making. Poindexter faced immense criticism from the media and politicians about the Policy Analysis Market project, a futures market that would have allowed trading in, and profiting from, such events as the assassination of heads of state and acts of terrorism. It is widely believe he will resign his position.