Francis went to the mountain of Laverna in 1224, two years before he died, to fast and pray in honor of the feast of St. Michael the Archangel (Sep. 29). The month of September is replete with images of the cross, including the Feast of the Exaltation of the Holy Cross (September 14). On September 17, Francis received the stigmata. The Legend of the Three Companions said:
"From that hour [after the locution at San Damiano], therefore, his heart was wounded and it melted when remembering the Lord’s passion. While he lived, he always carried the wounds of the Lord Jesus in his heart. This was brilliantly shown afterwards in the renewal of those wounds that were miraculously impressed on and most clearly revealed in his body. From then on, he inflicted his flesh with such fasting that, whether healthy or sick, the excessively austere man hardly ever or never wanted to indulge his body. Because of this he confessed on his death bed that he had greatly sinned against “Brother Body.” … We have told these things about his crying and abstinence in an incidental way to show that, after that vision and the message of the image of the Crucified, he was always conformed to the passion of Christ until his death." 
Thomas of Celano said that the cross that was imprinted internally on his soul at San Damiano would manifest itself externally on his body in the stigmata on Mount Laverna. “From that time on, compassion for the Crucified was impressed into his holy soul. And we honestly believe the wounds of the sacred Passion were impressed deep in his heart, though not yet on his flesh.”
There on Mount Laverna St. Francis prayed for two gifts: to feel in his body the pain which Jesus felt during his Passion and to know in his heart the love which Jesus felt for all humanity. And Francis, mysteriously, received the stigmata – the wounds of Christ – on his hands, feet, and side:
"On a certain morning about the feast of the Exaltation of the Cross, while Francis was praying on the mountainside, he saw a Seraph having six wings, fiery as well as brilliant, descend from the grandeur of heaven. And when in swift flight, it had arrived at a spot in the air near the man of God, there appeared between the wings the likeness of a man crucified, with his hands and feet extended in the form of a cross and fastened to a cross…. As the vision was disappearing, it left in his heart a marvelous fire and imprinted in his flesh a likeness of signs no less marvelous. For immediately the marks of nails began to appear in his hands and feet just as he had seen a little before in the figure of the man crucified." 
Francis was at once overwhelmed with joy, but doubled over with pain. The prayer that Francis made is remarkable. Francis had dedicated his life “carrying the cross” of Christ. The love of God that he discovered through the cross determined everything he did and how he lived his life. He loved Christ on the cross so much that he desired to be with him where he was – there on the cross. That is why he made this twofold prayer -- to feel in his body the pain of the cross, but also in his heart the love that Christ had for all people. In fact, there is a connection -- a oneness -- between sacrifice and charity. The cross, in fact, is the ultimate sacrifice, the ultimate charity of God.
The life of Francis was now inexplicably and mysteriously united to that of Christ. The Incarnation of Christ, the “masterpiece” of God’s creation, indeed, the whole purpose of creation (in the words of Scotus) culminated in the Passion and crucifixion as the highest expression of God’s love, charity, and mission: “When Jesus had taken the wine, he said, ‘It is finished.’ And bowing his head, he handed over the spirit” (John 19:30). The life, love, and mission of Christ were marked by the two great feasts of Christmas and Easter. Similarly, Francis’s life and devotion to Christ was defined by the two great events of the re-enactment of the nativity scene at Greccio (the Incarnation) and the reception of the stigmata at Laverna (the crucifixion).
Ultimately, the wounds of the stigmata were and remain a mystery. And as there were some who doubted at the time of Francis, so there remain those today who doubt it, as well. (Some have concluded that Francis had contracted leprosy). Yet, the stigmata remained a mystery also to St. Padre Pio who himself said that he himself did not understand the stigmata.
Finally, it is important to note that as Christians and Franciscans we do not put our hope solely in the cross. The cross was not the ultimate goal that the great saints sought: Heaven and the Resurrection were. The cross is not our final vocation: the Resurrection is. The cross is the mere pathway to the Resurrection. Without the cross there is no Resurrection; unless God comes down in the world, there is no way to go up to Heaven. Thus, in the end, suffering on the cross does not have the final word: the Resurrection does. By embracing the cross, Christ shows us the way. And Francis, by embracing it, is an example of how we should live.
 Legend Three Companions, Chap V
 2 Celano 10 (Book II: 249)
 Bonaventure, Major Life, chap. 13