Why is Mary John?
This answer is both covenantal
& discriminatory. 

The first appearance that we have is at the well, in John 4.  

We know that this is the author of the Gospel of John for multiple reasons, 

1- How else could we know what they spoke of, when no one asked him of it. 

2- because this is the only person that Jesus says speaks true, who is alive at the writing of the Gospel, and at the end of the of John 21 "we know this disciples testimony is true." 

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that she at the well is his wife, a Samaritan, 

1-they accuse him of having a devil and being a Samaritan. 

2- He only denies having the devil. not the being a Samaritan. 

3-but at the well, he makes a clear distinction between Jews and Samaritans. 

4- Where would they get the idea he is a Samaritan unless Mary, who would often kiss on him as stated in The Gospel of Phillip.

5- This is also the same reason that the woman caught in the very act of adultery is Mary. Why else would they follow her around to catch her in the very act, and why else would they not bring the man. Because they were following her to try and get Jesus to stone his friend or wife. The woman that was always hanging and kissing on him.