Rules 7.04c and 7.05 do it for me. Whether or not the ball is ruled "dead" or "out of play" would be irrelevant IF the lead runner on base misses a base in coming home. He would then forfeit not being able to be put out, and the play would not be considered over, until the missed base scenario is dealt with.
But the defensive team MUST appeal and touch the missed base with the ball. If the ump has seen the runner miss the base, he would then call the runner out for the third out, and the homerun is null and void.
Rule 7.04(c) NOTE: When a runner is entitled to a base without liability to be put out, while the ball is in play, or under any rule in which the ball is in play after the runner reaches the base to which he is entitled, and the runner fails to touch the base to which he is entitled before attempting to advance to the next base, the runner shall forfeit his exemption from liability to be put out, and he may be put out by tagging the base or by tagging the runner before he returns to the missed base.
7.05 Each runner including the batter-runner may, without liability to be put out, advance -- ?(a) To home base, scoring a run, if a fair ball goes out of the playing field in flight and he touched all bases legally; or if a fair ball which, in the umpire’s judgment, would have gone out of the playing field in flight, is deflected by the act of a fielder in throwing his glove, cap, or any article of his apparel;
Rule 7.05(i) Comment: The fact a runner is awarded a base or bases without liability to be put out does not relieve him of the responsibility to touch the base he is awarded and all intervening bases. For example: batter hits a ground ball which an infielder throws into the stands but the batter-runner missed first base. He may be called out on appeal for missing first base after the ball is put in play even though he was “awarded” second base.?If a runner is forced to return to a base after a catch, he must retouch his original base even though, because of some ground rule or other rule, he is awarded additional bases. He may retouch while the ball is dead and the award is then made from his original base.
But the defensive team MUST appeal and touch the missed base with the ball. If the ump has seen the runner miss the base, he would then call the runner out for the third out, and the homerun is null and void.
Rule 7.04(c) NOTE: When a runner is entitled to a base without liability to be put out, while the ball is in play, or under any rule in which the ball is in play after the runner reaches the base to which he is entitled, and the runner fails to touch the base to which he is entitled before attempting to advance to the next base, the runner shall forfeit his exemption from liability to be put out, and he may be put out by tagging the base or by tagging the runner before he returns to the missed base.
7.05 Each runner including the batter-runner may, without liability to be put out, advance -- ?(a) To home base, scoring a run, if a fair ball goes out of the playing field in flight and he touched all bases legally; or if a fair ball which, in the umpire’s judgment, would have gone out of the playing field in flight, is deflected by the act of a fielder in throwing his glove, cap, or any article of his apparel;
Rule 7.05(i) Comment: The fact a runner is awarded a base or bases without liability to be put out does not relieve him of the responsibility to touch the base he is awarded and all intervening bases. For example: batter hits a ground ball which an infielder throws into the stands but the batter-runner missed first base. He may be called out on appeal for missing first base after the ball is put in play even though he was “awarded” second base.?If a runner is forced to return to a base after a catch, he must retouch his original base even though, because of some ground rule or other rule, he is awarded additional bases. He may retouch while the ball is dead and the award is then made from his original base.