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What Biblical evidence is there that the Apostles feared for their lives after Jesus was crucified? A good answer will cite published commentary and/or provide in depth analysis of specific passages.

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Some commentators think so. John 20:19 is the best indication:

On the evening of that day, the first day of the week, the doors being locked where the disciples were for fear of the Jews, Jesus came and stood among them and said to them, “Peace be with you.” [ESV]

Thomas Constable's analysis is common:

The disciples had gathered in a secure room because they feared the Jewish authorities. The Jewish authorities had crucified their rabbi, so it was reasonable to think that they might come after them as well.

Adam Clarke suggests the fear was unfounded and due to lack of faith:

We do not find that the Jews designed to molest the disciples [...] but, as they had proceeded so far as to put Christ to death, the faith of the disciples not being very strong, they were led to think that they should be the next victims if found.

John Gill points out that they might also have feared being arrested for having stolen the body:

they might fear, that since they had took away their master's life, theirs must go next; and especially since it was rumoured abroad that they had stole away his body, they might be under the greater fear, that search would be made after them, and they be apprehended and brought into trouble on that account:

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Yes. First off, we know that Jesus told them to prepare to defend themselves and see to their own safety. Shortly thereafter, he was imprisoned, taken to trial in what would today be called a "kangaroo court", convicted on trumped-up charges, and put to death. His inner circle would definitely have every reason to fear for their own safety, and indeed John chapter 20 tells us that at the time of the Resurrection, they were meeting in a secure location with the doors locked for fear of the Jews. It doesn't get much clearer than that.

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