In the summer of 1588, John was elected third councillor to the vicar general for the discalced, Father NicolΓ‘s Doria, and had to return to Segovia in Castile, where in this capacity he was also prior. At his new site, one with a splendid view of Segovia and the surrounding area, he spent a good portion of his time again in manual labor, designing an addition to the monastery, quarrying stone for it, and working on its construction. He no longer wrote, but spent more time in prayer, going off to a cave on the property where he could view the countryside and have solitude for his deep contemplation. He had brought his latest work, The Living Flame of Love, to an unexpectedly swift close, confessing that he did not want to explain any further about the breathing of the Holy Spirit in the soul, "for I am aware of being incapable of so doing, and were I to try, it might seem less than it is. Never one to shun those who came for help, John continued his ministry of spiritual direction; the business matters of the order's government were always claiming attention as well. In fact, these latter sparked another conflict, this time among the discalced themselves. The clash began when NicolΓ‘s Doria called an extraordinary chapter in June 1590 for the purpose of undertaking two controversial moves. First he wanted to abandon jurisdiction over the nuns, a reprisal against Madre Ana de JesΓΊs who opposed his plans; Doria had hoped both to make changes in Teresa's constitutions and to govern the nuns through a body of councillors rather than through one friar appointed to the task. Second, he proposed the expulsion of Teresa's close collaborator, Father JerΓ³nimo GraciΓ‘n, from the discalced Carmelites. Fray John spoke in opposition to both moves. In the chapter the following year, different councillors were elected to assist Doria, and John remained without an office, a fact that was more a problem for others than for himself. When the news got about, some began raising strong protests. But John looked at things differently, as he so often did, and expressed his mind in a letter to the prioress in Segovia:
Do not let what is happening to me, daughter, cause you any grief, for it does not cause me any. What greatly grieves me is that one who is not at fault is blamed. Men do not do these things, but God, who knows what is suitable for us and arranges things for our own good. Think nothing else but that God ordains all, and where there is no love, put love, and you will draw out love [July 6, 1591].
Doria, in what seemed a rebuff, sent John of the Cross back into Andalusia, to an isolated monastery called La PeΓ±uela, a solitude like Duruelo or El Calvario. However, John was to stay there only in preparation for a mission to Mexico where he was to lead a group of 12 friars. He was happy in the solitude, but some ugly maneuverings began to disturb the peace of his friends, whom he had helped as spiritual director, and shattered the impressive silence of La PeΓ±uela. Fray Diego Evangelista, with bitter resentment against his former superior, was going about threatening and intimidating, trying to gather information against the spiritual friar so as to have him expelled from the discalced. Fray Diego never had time to proceed far with his designs. In mid-September John began to suffer a slight fever caused by an inflammation of the leg. Thinking it nothing serious, he paid little attention, but when it persisted he was forced to make the journey to Ubeda for the medical assistance that was unavailable at La PeΓ±uela. Given the choice between Baeza and Ubeda, he chose Ubeda, "for at Baeza they know me very well, and in Ubeda nobody knows me. " It was the last journey of his life.
The prior of the monastery at Ubeda, Fray Francisco CrisΓ³stomo, did not welcome the sick man. Learned and famous as a preacher, Fray CrisΓ³stomo had his weaknesses, among them a tendency to be mean and rigid. A sick friar was a nuisance and an expense as far as he was concerned, and he showed his vexation; nor did he care for people who were supposedly holy. John's sickness grew worse. His leg was already ulcerated, and the disease, erysipelas, spread to his back where a new fist-sized tumor formed. On December 13, Fray John of the Cross, knowing that time was running short, called for the prior and begged pardon for all the trouble he had caused. This profoundly changed the prior, who himself then begged forgiveness and left the cell in tears, totally transformed. According to witnesses Fray Francisco CrisΓ³stomo later died in the odor of sanctity. That same night, when the friars began to recite the prayers for the dying, Fray John of the Cross begged, "No, read some verses from the Song of Songs, " and then exclaimed, "Oh, what precious pearls! " At midnight, without agony, without struggle, he died, repeating the words of the psalmist: "Into your hands, O Lord, I commend my spirit. " The favors he had asked for in his last years he had now received: not to die as a superior, to die in a place where he was unknown, and to die after having suffered much.