Did the Apostle John die a natural death?

Century IX.

From the Chronicon of George Hamatolos (the sinner), codex Coislinianus 305 (Lightfoot-Holmes 6):

Μετα δε Δομετιανον εβασιλευσε Νερουας ετος εν, ος ανακαλεσαμενος Ιωαννην εκ της νησου απελυσεν οικειν εν Εφεσω. μονος τοτε περιων τω βιω εκ των δωδεκα μαθητων και συγγραψαμενος το κατ αυτον ευαγγελιον, μαρτυριου κατηξιωται. Παπιας γαρ ο Ιεραπολεως επισκοπος αυτοπτης τουτου γενομενος εν τω δευτερω λογω των κυριακων λογιων φασκει οτι υπο Ιουδαιων ανηρεθη, πληρωσας δηλαδη μετα του αδελφου την του Χριστου περι αυτων προρρησιν και την εαυτων ομολογιαν περι τουτου και συγκαταθεσιν.

And, after Domitian, Nerva ruled as king for one year[18 September 96 – 25 January 98], who, having called John back from the island, released him to house in Ephesus. Being then the only one still alive from the twelve disciples, and having composed the gospel according to himself, he was held worthy of martyrdom. For Papias, the bishop of Heirapolis, who was the eyewitness of this man, in the second volume of the lordly oracles claims that he was done away with by Jews, having clearly fulfilled with his brother the prediction of Christ about them and their own confession about this and submission.

Ειπων γαρ ο κυριος προς αυτους· δυνασθε πιειν το ποτηριον ο εγω πινω; και κατανευσαντων προθυμως και συνθεμενων. το ποτηριον μου, φησι, πιεσθε και το βαπτισμα ο εγω βαπτιζομαι βαπτισθησεσθε. και εικοτως, αδυνατον γαρ θεον ψευσασθαι. ουτω δε και ο πολυμαθης Ωριγενης εν τη κατα Ματθαιον ερμηνεια διαβεβαιουται ως οτι μεμαρτυρηκεν Ιωαννης, εκ των διαδοχων των αποστολων υποσημαιναμενος τουτο μεμαθηκεναι. και ο πολυιστωρ Ευσεβειος εν τη εκκλησιαστικη ιστορια φησι· Θωμας μεν την Παρθιαν ειληχεν· Ιωαννης δε την Ασιαν, προς ους και διατριψας ετελευτησεν εν Εφεσω.

For the Lord said to them: Are you able to drink the cup that I drink? And they assented desirously and agreed. My cup, he says, you shall drink, and you shall be baptized the baptism with which I am baptized. And reasonably, for God is unable to pass falsehood. And thus also the very learned Origen in the interpretation according to Matthew confirms as that John has been martyred, having signaled that he learned this from the successors of the apostles. And the well-read Eusebius in the ecclesiastical history says: Thomas was allotted Parthia, and John Asia, where also, having passed his time, he came to his end in Ephesus.

Here we see that Papias is the only named firsthand testimony to John having been martyred. But, in that he gives no details whatsoever--other than blaming it on Jews--historians now generally claim, on the sole basis of tertiary witnesses, that John died a natural death. What's interesting, though, is that the ancient historians who commented on this saw it as a fulfillment of prophecy: that John had to die a martyr, due to Jesus having said that he would indeed drink of His cup, and be baptised with His baptism.