Richard III has been deemed a “monster” by history. One of his great sins, reputedly, was the murder of his nephews, the princes in the Tower.
Now, admittedly, Richard was in charge when said murder would have occurred. And with either of these boys alive, he could not have held the crown in his own right unless he managed to demonstrate that either they, or their father the previous king, was illegitimate (which would have involved him basically calling his mother a cheating liar). And Richard seems to have been a pretty ruthless guy.
But there were other beneficiaries of their death, namely Henry Tudor (Henry VII), whose mother, Margaret Beaufort, seemed pretty determined to do whatever was necessary to get him to the throne (including marrying him to the princes’ sister, Elizabeth of York, who actually had a better claim to the throne than him but was obviously a girl and whose path to the succession therefore would have been at least somewhat frought). With either of these boys alive (as well as Richard, whose death in battle put Henry on the throne), Henry VII doesn’t make it to the throne (at least not as swiftly as he did, or in that timeframe). Without being in a position to ascend to it, he doesn’t get to marry Elizabeth of York, marriage to whom also did a lot to guarantee his accession. Henry VII had the opportunity to look into their disappearance, but even with his opportunity to do so and his ability as king to compel people to fess up, we never have gotten close to a real answer as to what happened. Now, maybe that is because what really happened, if exposed, would have caused the War of the Roses to flare up again, and that wasn’t a cost Henry was prepared to accept because it would have been so disastrous for England. Or maybe it’s because he/his mother had a hand in it, and that simply could not have been allowed to be seen to be the case. Subsequently, we have Tudor loyalists (especially Shakespeare) going out of his way to pin the deaths on Richard, who was long dead with no one to argue.
A mock trial was held some time ago, in which Richard was acquitted of the murders. This seems plausible, or at least it’s plausible that someone other than him/someone not acting on his behalf did it. Margaret Beaufort seems like a viable suspect.