With the loss of Jerusalem and Acre in 1187, the Knights of St John were left with their main strongholds of Krak des Chevaliers, Belvoir and Margat where the based themselves until Guy de Lusignan, King of Jerusalem recaptured Acre on 13 July 1191, which then became the capital of the Christian kingdom. Soon after the Order moved its headquarters to Acre. The Third Crusade that followed consolidated the coastal area of Outremer, but internecine fighting between the Christians weakened their position throught the 4th and 5th Crusades, until the Western Emperor, Frederick II "Stupor Mundi" took matters in hand and, in the face of an edict of excommunication, set out on his own Crusade. Instead of using his army against the Moslems, it was Frederick's intention to negotiate with the Egyptian Sultan for a peaceful territorial settlement in the Holy Land. Frederick proposed to use his army principally against the Latins in the East, to try to force them to acknowledge his position as regent and de facto ruler of the Latin states in the East.1

Through the Emperor's reputation and the weakness of  the Sultanate at that time, he succeeded in occupying Jerusalem itself under a settlement which left parts of the city, notably the former Templar sites, in the hand of the Muslims.  He took up residence in the old Hospital of St John and crowned himself King of Jerusalem in the Church of the Holy Sepulchre on 18 March 1229.2

With the departure of Frederick, Outremer returned to its previous parlous state with Christians intriguing against Christians until on 11 June 1244 Jerusalem fell for the last time to the Turks who swept through Palestine. Neither the Hospitallers not the Templars had returned to Jerusalem, preferring to remain in Acre where they had formed their little empires and also got involved in disputes among themselves

By 1271 the Hospitallers lost Krak des Chevaliers followed in 1285 by Margat. Acre finally fell in 1291 and the Hospitallers were compelled to abandon the Holy Land for the last time moving to Cyprus which became their next headquarters.

A first hand description of the last hours of Acre was given by the Grandmaster himself, Jean de Villiers in a moving letter written from his sickbed in  Cyprus to the Prior of St Gilles, Guillaume de Villaret, who was later to succeed to the Grandmagistry 

They [the Muslims] entered the city on all sides early in the morning and in very great force. We and our convent resisted them at St Anthony's Gate, where there were so many Saracens that one could not count them. Nevertheless we drove them back three times as far as the place commonly called 'Cursed'. And in that action and other where the brothers of our convent fought in defence of the city and their lives and country, we lost little by little all the convent of our Order, which is so much to be praised and which is close to Holy Church, and then came to an end. Among them our dear friend Brother Matthew de Clermont our marshal lay dead. He was noble and doughty and wise in arms. May God be gracious to him! On that same day the master of the Temple also died of a mortal wound from a javelin. God have mercy on his soul!

I myself on that same day was stricken nearly to death by a lance between the shoulders, a wound which has made the writing of this letter a very difficult task. Meanwhile a great crowd of Saracens were entering the city on all sides, by land and by sea, moving along the walls, which were all pierced and broken, until they came to our shelters. Our sergeants, lads and mercenaries and the crusaders and others gave up all hope and fled towards the ships, throwing down their arms and armour. We and our brothers, the greatest number of whom were wounded to death or gravely injured, resisted them as long as we could, God knows. And as some of us were lying as if we were half-dead and lay in a faint before our enemies, our sergeants and our household boys came and carried me, mortally wounded, and our other brothers away, at great danger to themselves. And thus I and some of our brothers escaped, as it pleased God, most of whom were wounded and battered without hope of cure, and we were taken to the island of Cyprus. On the day that this letter was written we were still there, in great sadness of heart, prisoners of overwhelming sorrow.

[Extract from: Cartulaire général de l'ordre des Hospitaliers, ed. Joseph Delaville le Roulx, no. 4157; translated by Edwin James King, The Knights Hospitallers in the Holy Land (London, 1931), pp. 301-2: amended by H. J. Nicholson.]

Avity, Pierre d'; Gottfried, Johann Ludwig: Archontologiae Cosmicae, Liber III: Origo Ordinum Militarium, tam Regularium, Dissertatio de Ordine Equitum Melitensum, pp.31-33 Frankfurt am Main, 1628

Delaville Le Roulx, Joseph  [Ed.]: Cartulaire général de l’ordre des Hospitaliers de Saint-Jean de Jérusalem, 1100-1310, 4 vols., Ernest Leroux, Paris,1884-1906

Foster, Michael John: A Short History of the Order of St. John of Jerusalem, Part One. The Order of St John of Jerusalem until 1798

Novare, Philip de : Les Gestes des Ciprois, No. 135-37, ed. Gaston Reynaud, (Geneva: Jules-Guillaumefick, 1887), 48-50, translated by James Brundage, The Crusades: A Documentary History, (Milwaukee, WI: Marquette University Press, 1962), 231-32

1. Novare, pp. 48-50

2. Foster, A Short History of the Order of St. John of Jerusalem