The council could not deny what had happened: "this man doeth many miracles." Gill says, "This is owned, and could not be denied by them." Their question is a call to action. Gill paraphrases it, "why is nothing done? why are we so dilatory? why do we sit still, and do nothing?" or else, "what is to be done?" They give their reason in the next breath: "If we let him thus alone, all men will believe on him: and the Romans shall come and take away both our place and nation" (John 11:48). Barnes asks why they did not believe if they admitted His miracles, and answers that "they did not doubt that impostors might work miracles." He thinks they were probably led to this by the wonders of the magicians in Egypt and by Deuteronomy 13:1. Matthew Henry says "they take it for granted that he is an enemy, and as such is to be run down."

Caiaphas, "the high priest that same year," answered: "Ye know nothing at all, Nor consider that it is expedient for us, that one man should die for the people, and that the whole nation perish not" (John 11:49-50). John explains that "this spake he not of himself," but "he prophesied that Jesus should die for that nation" and gather together "the children of God that were scattered abroad" (John 11:51-52). "Then from that day forth they took counsel together for to put him to death" (John 11:53). Jesus "walked no more openly among the Jews" and withdrew to Ephraim (John 11:54).

The "council" is the Greek synedrion, the Sanhedrin, which Barnes and Gill identify as the great ruling council of the nation. "Miracles" is semeia, signs, which is why the ESV says "many signs." The verb "do we" (poioumen) is present tense: "What are we doing?"

The Jews were then subject to Rome, as Barnes notes, and the council feared the Romans would "take away both our place and nation" (John 11:48). Barnes thinks "our place" probably refers to the temple.

Jesus' greatest sign led directly to the decision to kill Him. The leaders even plotted to put Lazarus to death, "Because that by reason of him many of the Jews went away, and believed on Jesus" (John 12:10-11). John later sums it up: "though he had done so many miracles before them, yet they believed not on him" (John 12:37).

Yet God was at work in the very council that opposed His Son. Caiaphas meant a political calculation, but John says he "prophesied" (John 11:51). Jesus would indeed die for the people, and not for that nation only, but to "gather together in one the children of God that were scattered abroad" (John 11:52). Their question, "What do we?", ended in a plan that God turned to accomplish salvation.