John Gill Commentary John 20:2

"She runneth therefore, and cometh to Simon Peter, and to the other disciple whom Jesus loved, and saith unto them, They have taken away the Lord out of the tomb, and we know not where they have laid him." — John 20:2 (ASV)

Then she runs and comes to Simon Peter
That is, after she had not only seen that the stone was taken away, but had looked into the sepulchre, and saw that the body of Christ was removed; for otherwise she could not have said, that it was taken away out of it: upon which she made all the haste she could to Peter; she knew where he was; and she was particularly bidden by the angel she saw in the sepulchre, to go to him:

and to the other disciple whom Jesus loved ;
John the writer of this Gospel; for these two were together, as they usually were; nor were they alone, for the rest of the disciples were with them:

and says to them, they have taken away the Lord out of the
sepulchre, and we know not where they have laid him .
The Oriental versions, the Syriac, Arabic, Persic, and Ethiopic, read, "I know not where they have laid him"; She could not say who had taken the body of Christ away, whether friends or enemies. Nor did she or any of the women with her know where it was put—whether in some other grave, exposed to insults, birds, or beasts of prey; whether laid in a more suitable or scandalous place; or whether this removal was for his greater honor or reproach. To know this gave her great concern and uneasiness, as she knew it must the disciples also.

So Christ, in a spiritual sense, may be removed from his people for a time, and they know not where he is; sometimes he removes himself, to chastise them for their former carriage, to try and exercise their grace, to inflame their love to him, and sharpen their desires after him, and to endear his presence to them the more, when they enjoy it again; sometimes he is taken away from them by preachers, when they leave him out of their discourses; and by their own sins and transgressions, which separate between him and them, with respect to communion; and who, for a time, may not know where to find him: and for the direction of such it may be observed, that he is to be found in the ministration of his word and ordinances in his churches.