D. John, according to Philip II's instructions, made a thorough examination of the fortifications and strategical position of Tunis, and had long talks about it with Gabrio Cervelloni, who was well versed in such matters; but, far from settling to dismantle the town, as the King thought, he decided to build a new fort, capable of holding 8000 men, to complete its defence. Tunis is situated on the banks of a lagoon, which is so shallow that it is called "el estaño" (the pond), which is no other than the ancient and famous port of Carthage, silted up by the centuries, and the carelessness and the filth of all Tunis which emptied itself there. The mouth of the lagoon is a narrow channel in the Gulf of Tunis, and it is in this opening that Goletta is situated, defending the entrance. On the opposite side there is an island, separated by another channel from Tunis, and it is here that D. John thought to build the new fort, with a covered communication with the Alcazaba. Most of those consulted warmly applauded the project, a few condemned it, faint-hearted ones or toadies, to whom not to agree with the King was openly to disobey him. But D. John, firm in his idea, ordered Gabrio Cervelloni to put it into execution without delay; which fact was not overlooked, and later the crafty Antonio Pérez, always on the watch, knew how to make capital out of it.
Meanwhile the Moors were reassured by the humane and generous conduct of D. John. They trusted him absolutely, and daily the fugitives returned to their houses, and Moors of the country descended from the mountains to sell bread, meat, eggs, olives, fish, beef, mutton, and a thousand other things, as peacefully and with as much confidence and security as they would in an ordinary market. There still remained, however, a garrison of Turks in Biserta; but the Moor Horrus, who was the Alcaide, surprised them with a few neighbours, and beheaded them all. He then took a fine Turkish galley which was in the port, killing some of the crew, making slaves of others, and giving liberty to the 156 Christian captives on board. Having accomplished this feat, the twenty-two Moorish magnates went to Tunis, with the Christian captives, to deliver them up to D. John, and to make their submission to him.
This happened on the 13th of October, and on the 14th D. John, satisfied as to the submission of the kingdom, publicly gave it over to the Prince Muley Hamet; not with the title of King of Tunis, but with that of Governor in the name of His Catholic Majesty D. Philip II, King of Spain. He also wrote the same day to Goletta, giving D. Juan de Cardona orders to embark on a galley for Palermo, and gave another as an escort to the dethroned King Muley Hamida and his son, and all the other Moors of his suite who cared to follow them. At first the proud Moor refused to embark, but, convinced by his son and by those about him that resistance would be futile, he allowed himself to be taken on the galley without resistance. He was wrapped in a long mulberry-coloured cloak, with a white burnous over it, with the hood drawn, hiding his face with its swollen features. He was swarthy, with an evil countenance and a scanty beard. He walked slowly and with much dignity, his arms crossed, and his eyes fixed on the African soil which he was treading for the last time. When he embarked on the galley from the boat he received a salute of two cannons, and the crew gave theirs also, which they called "de forzado." Then his African impassiveness broke down, and he burst into tears, saying bitterly in Arabic, "King without a crown, man without freedom, salutes are unbecoming to you." Such was the King Muley Hamida, whom Cervantes calls "the cruellest and bravest Moor in the world."
Tunis quieted and the Moors content with their new government, D. John returned to Goletta and began the preparations for his departure. He left 8000 men divided between Goletta, Tunis, Biserta and the island where they were beginning the new fort, and named as Generals of these garrisons D. Pedro Portocarrero, Gabrio Cervelloni, D. Francisco de Avila, and D. Juan Zagonera. This done, he embarked on the 24th of October in the evening, taking with him all the remainder of the army, except the Marqués de Santa Cruz, who remained with the galleys under his command as rearguard. At Palermo he learnt of the death of Princess Juana, which had taken place at the Escorial on the 8th of September. The loss of this beloved sister affected D. John very much, and those of his household saw him, in the privacy of his room, cry like a child, which proves that bravery and energy are not weakened by feelings and the tears which spring from pure and tender affections. He ordered funeral rites in the churches, and the fleet to go into mourning, painting and hanging with black the masts, yards, oars and bulwarks of the ships.
This mourning, however, did not prevent the great reception D. John received in Naples. It was something like the solemn triumphs of the Roman conquerors of old; nor did the procession lack captive kings and princes, to wit, Muley Hamida and his son, or strange wild beasts of other countries, represented by the lion Austria, who walked at D. John's stirrups, led by two strong Nubians who waited on it, without its seeming surprised or put out by the bands, salutes, or the shouting of the mixed multitude which accompanied D. John all the way from the mole to the palace.
D. John entered Naples on the 12th of November, and on the 13th Juan de Soto left for Rome on a secret mission, to tell the Pope from D. John that the Tunis expedition was ended as far as it concerned him, and that if the Pope still intended to give him the kingdom as he had offered to do, that he should interpose his good offices with Philip II, so that D. John might accept it without any disloyalty and with Philip's absolute consent. The ambassador D. Juan de Zúñiga knew of the arrival of Soto in Rome, and although he did not know the reason, he hastened to apprise Philip II of the fact, who by it was filled with suspicion and fresh jealousy. He was, however, soon enlightened, as in a day or two the Nuncio Ormanetto, Bishop of Padua, presented himself on a special mission on behalf of Gregory XIII, and explained very minutely the Pope's plans for the kingdom of Tunis and for D. John, urging strongly that they should be approved and favoured. D. Philip listened attentively, and as if these plans were not for the good of all Christendom, but only for the benefit of D. John of Austria. He thanked His Holiness very much for the interest that he took in his brother, and charged the Nuncio to say so to Gregory XIII.
Three days later he wrote a letter to his brother, of which Lorenzo Vander-Hammen makes a precis thus:
"That he was not to be anxious about his person or promotion, as he would see to that as of one so near to him, but that this was not the time until it was seen what would be the result of the past expedition, nor could it be of use or value, but rather a great vexation and care to all; that he would consider the matter well as the case demanded, and if it were advisable he would be the first to assist in its execution, as he desired it."