When Clay met reporters the day after he won the championship, he came off as a different man – more subdued, sober-tempered. "My mouth has overshadowed my ability," he said. One reporter asked, "Are you a card-carrying member of the Black Muslims?" Clay responded, "Card-carrying – what does that mean?...I know where I'm going, and I know the truth, and I don't have to be what you want me to be. I'm free to be what I want to be." It was a pivotal statement. "When I first heard that on television...," said boxing historian Gerald Early, "it was like an electric current went through me. I never heard a black man say anything like that, least of all an athlete." The new champion went on to declare that his name was no longer Clay; black American surnames were often inherited from the family names of white slaveholders. "I will be known as Cassius X." He was the shock of the new black, rejecting the authority of what was sacred in America. Cannon wrote that Clay was using boxing as "an instrument of mass hate...as a weapon of wickedness."
The world heavyweight champion's allegiance to the Nation of Islam disturbed many. Clay's father, for one, resented it deeply and claimed that the organization was taking a share of his son's money. (The Nation denied this, but Herbert Muhammad, the son of leader Elijah Muhammad, soon became Cassius's manager, charging as much as 40 percent of his income for services.) One night, a drunken Clay Sr. showed up at Cassius's training site with a knife, threatening to "kill all the Black Muslims." What the father didn't understand – or perhaps did, deepening his rage – was that his son had found in the Nation of Islam a new kind of family he hadn't known before. In Malcolm X, in particular, Cassius had discovered a comrade and role model, but it proved to be the most troubling relationship of his life. Cassius knew that tensions had recently emerged between the fiery minister and Elijah Muhammad. Malcolm had been growing disillusioned and was ready to move on. Others in the Nation, though, pointed to the friendship with Cassius Clay, "a fool fighter," as irresponsible on Malcolm's part. Leader Elijah Muhammad had believed there was "no way Clay could win" against Sonny Liston and wanted the Nation to keep a distance from him. Clay would have to choose between Malcolm's renegade ways and Elijah Muhammad's rule.
On March 8, 1964, Malcolm X spoke publicly of his separation from the Nation of Islam. He would start a new action group and hoped to work with other civil rights leaders – such as Dr. Martin Luther King Jr. – with whom he'd earlier been forbidden to work. In response, minister Louis Farrakhan, who had replaced Malcolm with Elijah Muhammad, pronounced that "hypocrites like Malcolm should have their heads cut off." Days later, Elijah Muhammad openly embraced Cassius and bestowed on him a new name: Muhammad Ali, meaning "beloved of God." (The New York Times, among others, refused for six years to acknowledge the honorific, still referring to Ali as Cassius Clay.) The young fighter's proud acceptance of the designation made plain his choice between the Nation of Islam and Malcolm X. The two former friends spoke only once more, later in the spring of 1964, during a chance encounter outside a hotel in Ghana. Malcolm told Ali, "Brother, I still love you, and you are still the greatest." Ali replied, "You left the Honorable Elijah Muhammad. That was the wrong thing to do, Brother Malcolm." Then Ali turned his back and walked away. Malcolm looked emptied. "I've lost a lot," he said to his companions. "A lot. Almost too much.... Be kind to him for his sake and mine. He has a place in my heart." In the months that followed, Ali sought to downplay the former friendship. "No one listens to Malcolm anymore," he told the press.
Ali and Sonny Liston were scheduled for a rematch in Boston on November 16, 1964, but three days prior to that, the young champion suffered an abdominal hernia, resulting in a five-month delay. On February 21, 1965, as Malcolm X stepped to a podium to speak to an audience at the Audubon Ballroom in Harlem, three men brandishing guns approached and shot him to death. Within minutes speculation spread that the Nation of Islam – particularly Louis Farrakhan – had been involved in, or sanctioned, the killing. (Farrakhan said in 2009, on 60 Minutes, "I may have been complicit in words that I spoke leading up to February 21 ...and regret that any word that I have said caused the loss of life of a human being.") That same night, Ali's Chicago South Side apartment caught fire. Some thought the event was an immediate strike against Ali for his rejection of Malcolm. Others, though, including Ali's young wife, Sonji, suspected that the blaze might be a warning from within the Nation of Islam that the boxer should stay faithful to his new family. In the years that lay ahead, Muhammad Ali would displace Malcolm X as one of America's most provocative observers of the paradoxes of racial life in America, even taking on similar speech cadences. But at the time, Ali expressed no sympathy for Malcolm X's death. It wasn't until 2004, in his book The Soul of a Butterfly: Reflections on Life's Journey, that Ali would say, "Turning my back on Malcolm X was one of the mistakes I regret most in my life. I wish I'd been able to tell Malcolm I was sorry."
The second Sonny Liston match proved even more startling than the first. In part owing to threats of violence and reprisals, Boston refused to reschedule the event; other cities also would not accept the meet. Promoter Harold Conrad finally booked the fight into a small youth center in the northeastern town of Lewiston, Maine.
Odds again heavily favored Liston. "Nobody was convinced," said Robert Lipsyte, "that Cassius Clay had really beat Sonny Liston." Ali entered the ring to loud booing and, after the bell sounded, took to circling Liston adeptly, as he had in the first match. What took place near the end of his eighth circle around Liston resulted in one of the most scrutinized and debated film clips of the 1960s. In a moment when Liston was hurling a clumsy punch and his balance was susceptible, Ali threw what looked like a swiping right graze at his opponent's head. Liston crumpled to the canvas, where he stayed for several seconds, sprawling, rolling, groping. It happened so fast that many thought it had never happened at all – that Liston had been dropped by what became known as the phantom punch. However, a video camera on the far side of the ring caught clearly the force of the impact: "You can see Liston's neck and his spine just shudder," said one analyst. Confusion overtook the moment. Referee Jersey Joe Walcott tried to shove Ali to a corner to begin a time count on Liston. Ali, though, was as shocked as everybody else. He towered over Liston, a gloved fist cocked, yelling, "Get up and fight, sucker!" Liston finally rose reluctantly, but he doubled over in fright when Ali resumed his assault. A moment later Walcott stopped the match, after learning that Liston had been on the mat long enough to be counted out. Ali had won his first defense of his heavyweight title in a minute and 42 seconds. The audience broke out in a loud chorus of booing. Liston, they thought, had thrown the match. Ali himself had doubts. "It was a good punch," he later said, "but I didn't think I hit him so hard he couldn't have got up."
Liston lived in Las Vegas for the next several years, maintaining ties to underworld crime, still fighting and winning matches, though never to any glory. On January 5, 1971, his wife, Geraldine, returned home from a holiday trip and found her husband slouched against their bed, dead of an apparent heroin overdose. Ali's biographer Hauser recounted a moment, years later, when Ali wished aloud that his early foe was still alive, that they might sit around and talk about what was past. After Hauser asked Ali what he would say to Liston, Ali replied, "Man, you scared me."