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According to Legacy.com his said his parents were dead
Morrison's official Elektra biography stated his parents were deceased. He told acquaintances he was an orphan. On the song "The End," he sang about killing his father to have a relationship with his mother. But George and Clara Morrison were not dead and, in fact, outlived their son by many years. Clara died in 2005, her husband in 2008. Before his death, George Morrison spoke to the author of the authorized biography The Doors by the Doors and appears on the DVD When You're Strange. "We look back on him with great delight," the older Morrison says on camera. He also speculates that his son distanced himself from his family because, "I had the feeling that he felt we'd just as soon not be associated with his career. He knew I didn't think rock music was the best goal for him. Maybe he was trying to protect us."
This is again retold by the American Conservative,
By then, the admiral and Jim had fallen out, polarized by years of mutual incomprehension and by the father’s harsh dismissal of the son’s career plans. When the Doors made it, Jim told reporters that his parents were dead.
The American Conservative says nothing of Jim's relationship to his parents other than this which says nothing of the career choice,
In fact, during Morrison’s time in Paris, the admiral had been on his mind. Alan Ronay, an old college friend, spent weeks with Jim there. “One night we had a conversation that was totally moving,” Ronay told Morrison biographers James Riordan and Jerry Prochnicky. “It was full of affection … Jim telling funny stories about his dad and so on. The stories were really tender and warm. I wish his parents could’ve heard it. I really felt that he’d totally reclaimed himself.” But a few months later, he was dead.
This interview with Jim's bodyguard Tony Funches touches on these exact questions,
Did Morrison ever discuss why he claimed to have no family? How did this estrangement with his parents affect him?
> No, and I didn't feel it was my place as a friend and/or employee to inquire further. When he did mention something related to that topic, it was obscure by design, ambiguous at best. All I knew for sure was that he had no warmth for his strictly authoritarian dad and was sad that his mom didn't negotiate a lessening of that authoritarianism. His siblings were of the sentiment that you go along to get along, so they might secretly support his antics and avocation, but at great peril in the household of Adm. Morrison.
> I did have the underlying sense that besides the above, he really didn't want to cause them greater embarrassment and/or engage in further friction. Besides, he was aware of what the media could and would do with widespread knowledge of the identity of this family. All this at a time of great social upheaval, with a charged atmosphere of anarchy and the FBI assassinating and/or framing every last Black Panther party member they could find…the days of rage and the Chicago Seven. Why would he want to bring his family into it?
And, another question from the same interview,
Do you think it would have been detrimental to the Doors' career had it been revealed that Morrison's father played a key role in the Vietnam War? Do you think that is why he claimed to be an orphan?
> Certainly not. No one beefed that Robby's dad ran The Rand Corporation! It would require a wide array of systemic morons to make that stretch. In fact, many of the rock and roll icons of the day were scions of wealthy and/or powerful families: Carly Simon (Simon and Schuster), Grace Slick went to Wesleyan College In ANY case a lot of people knew it anyway.
It seems as if never said anything about his estranged dad's career choice. Instead, Jim seems to have largely ignored that publicly.