On 9 April 1483 Edward IV died, leaving as heir and spare two preteen princes. Edward IV’s brother, Richard of Gloucester, was named protector; by late April Richard was making moves to consolidate his protectorate. Or seize the throne. You pick.
When Richard arrested members of her family in late April, the dowager Queen Elizabeth felt she and her children were in danger, so she and most of her children entered sanctuary at Westminster. This was her second flight to sanctuary; the first was in 1470.
Though she had her second son Richard with her, her eldest son, the uncrowned new king Edward V, did not join the rest of his family in sanctuary as he was already in Richard’s custody. By mid-May, he was lodged in the Tower for “safekeeping” preparing for his scheduled coronation in late June.
Uncle Richard also wanted (needed) to have the younger brother Richard in his custody, too – either in order to safeguard his protectorship against the queen’s relatives or in order to eliminate both boys in his plan to seize the throne (again, you choose: I personally opt for the latter).
Richard couldn’t politically afford an outright sanctuary breach – going into Westminster with armed men – to prise the young duke of York from the sanctuary. Chroniclers and historians, like Thomas More, later wrote about the discussions Richard and his councillors had about what to do.
More, in his later very anti-Richard drama about Richard III’s usurpation, gave Richard’s chief ally the duke of Buckingham a long speech to his fellow councillors about the evils of sanctuary, saying it allows criminals to escape just desserts. Besides, he said, there’s no need for sanctuary under a just leader, and surely Richard is a just leader.
Buckingham convinced his fellow councillors that Richard would never harm his own nephew; he was both a man of justice and a fond uncle. Though some historians have argued that in Buckingham’s speech More was voicing the objections of all “sensible laymen,” as one historian put it, to sanctuary….
…in the context of the storyline (where the reader knows Richard and his very evil henchman Buckingham intend to kill the innocent princes), More’s point is that sanctuary was the opposite of what Buckingham argued, a necessary bulwark against tyranny and political corruption.
Back to the story: convinced by Buckingham, a delegation headed by the archbishop of Canterbury went to Westminster to persuade the dowager queen to surrender her son to his uncle. They told her that the young duke of York needed to prepare for his brother’s coronation.
She agreed and sent her son off to join his brother in the Tower. Soon after in a series of rapid moves Richard had Parliament declare his nephews illegitimate and himself crowned as Richard III instead. The boys were never seen again – probably (I think) murdered at the order of their uncle.
The queen and her other children remained in sanctuary. Though it was very inconvenient for Richard to have them out of his reach, potentially lending dynastic legitimacy to a challenge, he (again) could not afford to breach the sanctuary and so left them there, heavily guarded. In March 1484 Elizabeth and her daughters emerged from the sanctuary. An argument that Richard III did not have his nephews killed is that Elizabeth and her daughters joined Richard III’s court; would Elizabeth have done that if she had believed Richard was guilty of her sons’ deaths? Or did she have a longer game plan?
For the history of sanctuary in England, Richard III’s usurpation and reign were very significant. Richard III’s reluctance to risk harm to his (very shaky) moral legitimacy by breaching sanctuary and committing violence in a sacral space augmented the protective power of those spaces. Increasingly opponents to his regime fled to sanctuary to escape execution; reportedly in 1485 when Henry Tudor landed to overthrow Richard III, men poured out of the sanctuaries to join him. Henry VII, once on the throne, advertised himself as protector of sanctuary to demonstrate his opposition to tyranny.
For sources on all this – see Vergil, English History, 175–78, 210; Fabyan, New Chronicles, 668; More, Historie of Richard the Thirde, in Complete Works vol. 2 (Yale UP 1963), and others cited in my Seeking Sanctuary.