A Navy officer who was dismissed last month as commander of a Connecticut-based nuclear submarine faked his own death to end an affair he was carrying on with a mistress, investigation documents show. 
 
 In this Aug. 3, 2012 photo provided by the U.S. Navy, Cmdr. Michael P. Ward II, center, is saluted during the change-of-command ceremony for the nuclear submarine, USS Pittsburgh, at the Naval Submarine... (Associated Press) 
 
 Navy Cmdr. Michael P. Ward II was relieved of his duties aboard the USS Pittsburgh a week after taking command of the attack submarine. 
 
 Investigators found that Ward sent his mistress an email from a fictitious person named "Bob" in July, saying that Ward had died unexpectedly, according to a report obtained Tuesday by The Associated Press through a Freedom of Information Act request. 
 
 Navy Lt. Cmdr. Jennifer Cragg, a spokeswoman for the Pittsburgh's submarine group in Groton, said Ward has received a letter of reprimand for adultery and other military violations, and paperwork has been filed to remove him from the Navy. 
 
 Details of the affair were first reported by The Day of New London. 
 
 Ward, who is currently assigned to a submarine group in Groton, has not responded to requests for comment. 
 
 The woman learned that Ward was still alive when she turned up at Ward's former residence in Burke, Va., to offer condolences. The new owner told her that Ward had moved to Connecticut to take command of a submarine. 
 
 "She was very surprised," Jon Boyle, the new owner, said in a telephone interview. 
 
 Boyle said the woman was accompanied by another woman with a child in tow. "She told me they were good friends and they'd known him a while." 
 
 Ward, who had been working at the Joint Chiefs of Staff in Washington, met the woman through an online dating service in October and used an alias to communicate with her by email, the investigation report says. The married officer visited her during trips to the Norfolk, Va., area for training and they spent a weekend together in Williamsburg, Va., in November. The woman was not named. 
 
 After moving to Connecticut, Ward learned that his mistress was pregnant. In late July, he met with her to discuss how to handle the pregnancy. Soon afterward the woman lost the baby due to complications, the investigation report says. 
 
 Ward was found guilty of Uniform Code of Military Justice violations including dereliction of duty, unbecoming conduct and adultery, and received the punitive letter of reprimand, Cragg said. 
 
 U.S. Rep. Joe Courtney, a Democrat whose eastern Connecticut district includes the submarine base, said it was a sad situation. 
 
 "The Navy doesn't kid around with its leadership," Courtney said. "These positions, to command submarines, are very competitive and I think the Navy is right to hold people to the highest standard." ||||| Navy Cmdr. Michael P. Ward II, who has been accused of having an affair with a 23-year-old Chesapeake, Va., woman and faking his death as a means of ending it, has been relieved of his duties as the commanding officer of the USS Pittsburgh, just one week after he was put in command. 
 
 
 
 The woman said she met Ward, 43, on a dating website in October. She said Ward, who is married with children, told her her he was separated and that he worked in "special ops." She said he got her pregnant then, in an effort to end the relationship, faked his death in an email communication in July. 
 
 
 
 The woman talked to The Day under the condition that her name would not be used. Reached by telephone Sunday afternoon, Ward, who lives in Gales Ferry, declined to comment. 
 
 
 
 According to a press release from the Navy, Capt. Vernon Parks, commander of Submarine Development Squadron 12, relieved Ward on Friday "due to lack of confidence in Ward's ability to command based upon allegations of personal misconduct on the part of Ward." 
 
 
 
 "Our Navy has a very clear and unambiguous standard regarding the character of our commanding officers, spelled out in the Charge of Command. I reviewed this Charge with Cmdr. Ward before he assumed command. He understood the Navy's high standards for command leadership and he failed to uphold them," Parks said. 
 
 
 
 Cmdr. Michael Savageaux has taken command of the USS Pittsburgh. He was the commanding officer before Ward assumed command on Aug. 3. Ward has been reassigned to administrative duties on the staff of Commander, Submarine Group Two. 
 
 
 
 Lt. Cmdr. Jennifer Cragg of Submarine Group Two said the Navy would not be releasing details of the investigation until it is complete. 
 
 
 
 The Virginia woman, who works in the banking industry, asked not to be identified because she does not want to jeopardize her career. 
 
 
 
 "I don't want revenge here," the woman said in a telephone interview Sunday. "I want everyone to know the truth about Michael. He does not need to be commanding a submarine. He's a deceitful man." 
 
 
 
 The woman said she has been in contact with the Naval Criminal Investigative Service and with the master chief of the USS Pittsburgh. She provided The Day with copies of text messages and emails from Ward. 
 
 
 
 "I want you, but I don't know how to make this all perfect," one of the texts says. Another says, "I love you and I always will." 
 
 
 
 The woman said Ward sent her emails using the name Tony Moore, explaining that he had to use the name because of his position in the special forces. She said Ward told her his real name after they met. 
 
 
 
 On July 6, she received an email from his address purporting to be from a man named Bob who worked with Ward. 
 
 
 
 "He asked me to contact you if this ever happened," the email says. "I am extremely sorry to tell you that he is gone. We tried everything we could to save him. I cannot say more. I am sorry it has to be this way." 
 
 
 
 The email goes on to say, "He loved you very much," and that Bob had something Ward had wanted to give to her. 
 
 
 
 The woman said that on July 9, she drove with her family members to Ward's house in Burke, Va., to pay her respects and learned from the new owner that Ward was alive and had moved to Connecticut to take command of a submarine. 
 
 
 
 She said she became ill, was hospitalized, and learned she was pregnant. She said she has since lost the baby. 
 
 
 
 Ward, a Buffalo, N.Y., native, joined the Navy in 1987. He had served on the Joint Chiefs of Staff at the Pentagon. He said, upon taking command of the USS Pittsburgh last week, that it was the culmination of a lifelong dream. 
 
 
 
 The USS Pittsburgh, a Los Angeles-class attack submarine that was commissioned in 1985, returned to Groton in June following a six-month deployment that included stops in Bahrain, the United Arab Emirates and Spain. 
 
 
 
 k.florin@theday.com 
 
 
 
 j.mcdermott@theday.com ||||| WASHINGTON — A month before a murderous rampage at the Washington Navy Yard, Aaron Alexis called the police in Rhode Island to complain that he had changed hotels three times because he was being pursued by people keeping him awake by sending vibrations through the walls. 
 
 When officers came to his hotel room early on Aug. 7, Mr. Alexis told them that a person he had argued with at an airport in Virginia “has sent three people to follow him” and that they were harassing him with a microwave machine, according to a Newport, R.I., police report. Mr. Alexis said he had heard “voices speaking to him through the wall, flooring and ceiling,” the report said. 
 
 Mr. Alexis told the police he was a Navy contractor, and then twice that month he sought treatment from the Veterans Affairs Department for psychiatric issues, according to a senior law enforcement official. But it did not raise a red flag that might have prevented him from entering the military base in Washington where, the authorities say, he killed 12 people on Monday. 
 
 On Wednesday, Mr. Alexis’s mother apologized to the victims in a brief statement she read from her Brooklyn home. 
 
 “I don’t know why he did what he did, and I will never be able to ask him why,” Cathleen Alexis said. “Aaron is now in a place where he can no longer do harm to anyone, and for that I am glad. To the families of the victims: I am so so very sorry that this happened. My heart is broken.” 
 
 The episode in Rhode Island adds to a growing list of questions about how Mr. Alexis, who had a history of infractions as a Navy reservist, mental health problems and run-ins with the police over gun violence, gained and kept a security clearance from the Defense Department that gave him access to military bases, including the navy yard, where he was shot to death by the police. 
 
 Time and again, Mr. Alexis’s behavior fell below a level that would have brought a serious response, like a less-than-honorable discharge from the military or involuntary commitment to a mental institution, experts and officials said. 
 
 But the sheer number of episodes raises questions about the government’s system for vetting people for security clearances, including the thousands of contractors who help run the nation’s military and security system work. Though the cases are different, the access granted Mr. Alexis, a former Navy reservist who as an independent contractor serviced Navy computers, raises questions similar to those raised about another outside government contractor, Edward J. Snowden, who leaked national intelligence secrets. 
 
 “These two incidents combined suggest to me a very flawed system for granting security clearances,” said Senator Susan Collins, Republican of Maine, who called for a Congressional investigation into the granting of security clearances to government contractors. “Who knows how many other Snowdens and Aaron Alexises are out there?” 
 
 On Tuesday, President Obama ordered the White House budget office to conduct a governmentwide review of policies for security clearances for contractors and employees in federal agencies. In an interview with Noticias Telemundo, the president said the nation did not have a “firm enough background check system.” He also called once again for Congress to enact legislation to keep guns out of the hands of criminals and those with mental illness. 
 
 “I do get concerned that this becomes a ritual that we go through every three, four months, where we have these horrific mass shootings,” he said. 
 
 Senior Pentagon officials also said that Defense Secretary Chuck Hagel intended to review physical security and access at all Defense Department installations around the world. 
 
 Many planets aligned to place Mr. Alexis, 34, at the start of the workday in the navy yard with a Remington pump-action shotgun, firing down from a balcony, the police said, and killing the employees, all civilians. 
 
 As an honorably discharged veteran, he cleared a basic hurdle to receive a Defense Department security pass. Despite his being investigated by police departments in Seattle and Fort Worth, for firing a gun in anger, no charges were filed that would have shown up in his F.B.I. fingerprint file. Despite mental health issues — he twice went to Veterans Affairs hospitals last month seeking treatment for insomnia — he was never committed and so was legally able in Virginia to buy the weapon the police said he used in the shootings. 
 
 “The system didn’t pick up the red flags because the red flags in this case had not been fed into the system,” one Pentagon official said. “Perhaps we need to look at the ‘filters,’ and whether some sorts of behaviors and incidents, even if they do not rise to the level of punishment, should nonetheless be part of the files for review.” 
 
 Law enforcement officials on Tuesday provided new details about the shooting. They said that in addition to the shotgun Mr. Alexis was carrying, he used a .45-caliber handgun that he may have picked up once inside the Navy base. 
 
 The Washington police chief, Cathy Lanier, said that officers armed with AR-15s were at the scene within two minutes of the first 911 call. But some reported to the wrong building because callers had misidentified the building. Chief Lanier said the entire shooting episode lasted at least 30 minutes. 
 
 The gunman was identified by an F.B.I. agent holding a machine to the fingers of the dead body. Within seconds, it identified Mr. Alexis from fingerprints on file because of his military service. 
 
 In the search for more information — and especially the unanswered question of motive — federal and local authorities have interviewed hundreds of people and are poring through the contents of Mr. Alexis’s Yahoo e-mail account. 
 
 Mr. Alexis had shown a “pattern of misbehavior” during his four years as a reservist, according to Navy officials. That pattern caused some of his commanders to consider giving him a general discharge — one level below honorable, which could have derailed his security clearance. 
 
 Instead, Mr. Alexis received an honorable discharge from the military in January 2011, after he had applied for an early discharge under the Navy’s “early enlisted transition program.” A major reason, officials said, was that his misbehavior in the Navy was not violent. It included insubordination, traffic violations and being absent without leave — two days he spent in jail after a fight in a bar in DeKalb County, Ga. 
 
 Mr. Alexis was also twice investigated by other police departments in shooting episodes — once for firing through his ceiling in Fort Worth, Tex., and another time for shooting out a car’s tires in Seattle, during what he described as an anger-fueled blackout. 
 
 Mr. Alexis, who worked for an independent contractor called the Experts, worked on half a dozen military bases from North Carolina to Rhode Island this year, said the company’s chief executive, Thomas E. Hoshko. If he had known of the police reports about Mr. Alexis that have surfaced in the news, “we would have never looked at him,” Mr. Hoshko said. 
 
 In any event, it was the responsibility of the Defense Department to grant Mr. Alexis his security credential allowing him onto bases, known as a Common Access Card. Pentagon officials said the Navy was responsible for his clearance, using a check of F.B.I. records and another database with the Office of Personnel Management. 
 
 Mr. Alexis left the Experts to attend school in January 2013, Mr. Hoshko said, but returned in July, when he again passed a drug test and a background check and received a secret clearance from the Defense Department. 
 
 Mr. Alexis’s clearance was a midlevel designation required for many military jobs, officials said. A secret clearance does not require as extensive a background investigation as a top-secret clearance, can be completed in one to three months and is good for 10 years. Among the factors that can disqualify someone are conviction for a felony, illegal drug use and financial problems. 
 
 Mr. Alexis’s father told the police after the Seattle shooting in 2004 that his son suffered post-traumatic stress symptoms after volunteering in the rescue after the attack on the World Trade Center on Sept. 11, 2001. 
 
 Colleagues who worked with Mr. Alexis at that time in a computer support center at Manhattan Borough Community College, near ground zero, did not recall him volunteering or mentioning Sept. 11. 
 
 One co-worker, Barry R. Williams, said Mr. Alexis had held onto grudges. “Some small thing would happen, something so small I couldn’t even remember the details, but two, three weeks later he’d still be bringing it up, be upset about it,” Mr. Williams said. 
 
 In White Settlement, Tex., the Fort Worth suburb where Mr. Alexis lived in recent years when he was not traveling for work, he told a friend, Melinda Downs, that he had post-traumatic stress disorder, and that it caused him to be withdrawn and suffer from insomnia. He once went three days without sleep, said Ms. Downs, who owns a barber shop. 
 
 After the police in Newport responded to Mr. Alexis’ call for help on Aug. 7, a sergeant who reviewed the report, Frank C. Rosa Jr., contacted the Newport naval base police and faxed a copy of Mr. Alexis’s wild statements. It is unclear whether the account made it up the chain of command. 
 
 On Aug. 23, Mr. Alexis went to Veterans Affairs hospitals in Providence, where he had been working as a contractor, complaining of insomnia but did not say that he was hearing voices, according to a senior federal official. Mr. Alexis said he could not sleep for more than a few hours. Doctors there prescribed him an antidepressant pill commonly prescribed for insomnia, Trazodone, the official said. 
 
 Five days later, Mr. Alexis went to a Veterans Affairs hospital in Washington, where he had traveled to work on a job at the navy yard. Mr. Alexis, who had not been given many Trazodone pills in Providence, said to the medical personnel in Washington that he was still having trouble sleeping and the doctors prescribed him more Trazodone, said the official. 
 
 In that meeting, Mr. Alexis told the medical personnel that he was not using drugs, did not have suicidal thoughts, was not depressed or particularly anxious, and was not having nightmares, the official said.
– The commander of a nuclear submarine tried to concoct an ingenious plan to get himself out a jam, but the Hunt for Red October this is not. The Navy says Cmdr. Michael P. Ward II tried to end an affair by sending a fake email from a guy named "Bob" to his mistress saying he had been killed, reports AP. The airtight plan began to unravel when she showed up at his residence as a friend to offer condolences. As a result, the Navy has relieved Ward as commanding officer of the USS Pittsburgh, a position he held for all of a week. He also might be booted from the Navy on a slew of related military violations. The unidentified mistress tells Connecticut newspaper The Day that the married-with-children Ward sent the fake email after she got pregnant. "I don't want revenge here," she says. "I want everyone to know the truth about Michael. He does not need to be commanding a submarine. He's a deceitful man."