In 1221, so some writers tell us, Francis drew up a new rule for the Friars Minor. Others regard this so-called Rule of 1221 not as a new rule, but as the first one which Innocent had orally approved; not, indeed, its original form, which we do not possess, but with such additions and modifications as it has suffered during the course of twelve years. However this may be, the composition called by some the Rule of 1221 is very unlike any conventional rule ever made. It was too lengthy and unprecise to become a formal rule, and two years later Francis retired to Fonte Colombo, a hermitage near Rieti, and rewrote the rule in more compendious form. This revised draft he entrusted to Brother Elias, who not long after declared he had lost it through negligence. Francis thereupon returned to the solitude of Fonte Colombo, and recast the rule on the same lines as before, its twenty-three chapters being reduced to twelve and some of its precepts being modified in certain details at the instance of Cardinal Ugolino. In this form the rule was solemnly approved by Honorius III, 29 November, 1223 (Litt. "Solet annuere" ). This Second Rule, as it is usually called or Regula Bullata of the Friars Minor, is the one ever since professed throughout the First Order of St. Francis (see RULE OF SAINT FRANCIS). It is based on the three vows of obedience, poverty, and chastity, special stress however being laid on poverty, which Francis sought to make the special characteristic of his order, and which became the sign to be contradicted. This vow of absolute poverty in the first and second orders and the reconciliation of the religious with the secular state in the Third Order of Penance are the chief novelties introduced by Francis in monastic regulation.
It was during Christmastide of this year (1223) that the saint conceived the idea of celebrating the Nativity "in a new manner", by reproducing in a church at Greccio the praesepio of Bethlehem, and he has thus come to be regarded as having inaugurated the population devotion of the Crib. Christmas appears indeed to have been the favourite feast of Francis, and he wished to persuade the emperor to make a special law that men should then provide well for the birds and the beasts, as well as for the poor, so that all might have occasion to rejoice in the Lord.
Early in August, 1224, Francis retired with three companions to "that rugged rock 'twixt Tiber and Arno", as Dante called La Verna, there to keep a forty days fast in preparation for Michaelmas. During this retreat the sufferings of Christ became more than ever the burden of his meditations; into few souls, perhaps, had the full meaning of the Passion so deeply entered. It was on or about the feast of the Exaltation of the Cross (14 September) while praying on the mountainside, that he beheld the marvellous vision of the seraph, as a sequel of which there appeared on his body the visible marks of the five wounds of the Crucified which, says an early writer, had long since been impressed upon his heart. Brother Leo, who was with St. Francis when he received the stigmata, has left us in his note to the saint's autograph blessing, preserved at Assisi, a clear and simple account of the miracle, which for the rest is better attested than many another historical fact. The saint's right side is described as bearing on open wound which looked as if made by a lance, while through his hands and feet were black nails of flesh, the points of which were bent backward. After the reception of the stigmata, Francis suffered increasing pains throughout his frail body, already broken by continual mortification. For, condescending as the saint always was to the weaknesses of others, he was ever so unsparing towards himself that at the last he felt constrained to ask pardon of "Brother Ass", as he called his body, for having treated it so harshly. Worn out, moreover, as Francis now was by eighteen years of unremitting toil, his strength gave way completely, and at times his eyesight so far failed him that he was almost wholly blind. During an access of anguish, Francis paid a last visit to St. Clare at St. Damian's, and it was in a little hut of reeds, made for him in the garden there, that the saint composed that "Canticle of the Sun", in which his poetic genius expands itself so gloriously. This was in September, 1225. Not long afterwards Francis, at the urgent instance of Brother Elias, underwent an unsuccessful operation for the eyes, at Rieti. He seems to have passed the winter 1225-26 at Siena, whither he had been taken for further medical treatment. In April, 1226, during an interval of improvement, Francis was moved to Cortona, and it is believed to have been while resting at the hermitage of the Celle there, that the saint dictated his testament, which he describes as a "reminder, a warning, and an exhortation". In this touching document Francis, writing from the fullness of his heart, urges anew with the simple eloquence, the few, but clearly defined, principles that were to guide his followers, implicit obedience to superiors as holding the place of God, literal observance of the rule "without gloss", especially as regards poverty, and the duty of manual labor, being solemnly enjoined on all the friars. Meanwhile alarming dropsical symptoms had developed, and it was in a dying condition that Francis set out for Assisi. A roundabout route was taken by the little caravan that escorted him, for it was feared to follow the direct road lest the saucy Perugians should attempt to carry Francis off by force so that he might die in their city, which would thus enter into possession of his coveted relics. It was therefore under a strong guard that Francis, in July, 1226, was finally borne in safety to the bishop's palace in his native city amid the enthusiastic rejoicings of the entire populace. In the early autumn Francis, feeling the hand of death upon him, was carried to his beloved Porziuncola, that he might breathe his last sigh where his vocation had been revealed to him and whence his order had struggled into sight. On the way thither he asked to be set down, and with painful effort he invoked a beautiful blessing on Assisi, which, however, his eyes could no longer discern. The saint's last days were passed at the Porziuncola in a tiny hut, near the chapel, that served as an infirmary. The arrival there about this time of the Lady Jacoba of Settesoli, who had come with her two sons and a great retinue to bid Francis farewell, caused some consternation, since women were forbidden to enter the friary. But Francis in his tender gratitude to this Roman noblewoman, made an exception in her favour, and "Brother Jacoba", as Francis had named her on account of her fortitude, remained to the last. On the eve of his death, the saint, in imitation of his Divine Master, had bread brought to him and broken. This he distributed among those present, blessing Bernard of Quintaville, his first companion, Elias, his vicar, and all the others in order. "I have done my part," he said next, "may Christ teach you to do yours." Then wishing to give a last token of detachment and to show he no longer had anything in common with the world, Francis removed his poor habit and lay down on the bare ground, covered with a borrowed cloth, rejoicing that he was able to keep faith with his Lady Poverty to the end. After a while he asked to have read to him the Passion according to St. John, and then in faltering tones he himself intoned Psalm cxli. At the concluding verse, "Bring my soul out of prison", Francis was led away from earth by "Sister Death", in whose praise he had shortly before added a new strophe to his "Canticle of the Sun". It was Saturday evening, 3 October, 1226, Francis being then in the forty-fifth year of his age, and the twentieth from his perfect conversion to Christ.