1048-1051 AD:
The time John spent training his soldiers also gave him time to fully consider his strategy against the Turks. If he sent an entire army against these marauders, they could pick away until there was nothing left, or they might be lured into an ambush and routed, if not destroyed. He thanked God for the 50,000-strong local militia in Armenia. John would decide to utilise the terrain to his advantage. This campaign would be decided, not by the Kataphractoi and Skoutatoi, but by the Akritae and the Hippo-toxotai, the skirmishers and horse-archers. Following the advice of the Roman dictator, Quintus Fabius Maximus, John decided that the best way to fight these marauding bands of Muslim fanatics was to not be drawn into open battle.
This strategy appeared to work. The Seljuks could not bait the Romans out of their cities and fortresses and could not assault the walls in time before news of a larger force approaching reached them. As for the nomads, they lived off the land, so the land was where the traps would be set. Any attempts to penetrate into Anatolia were usually foiled at the Taurus Mountains. One group that made it as far as Iconium was personally destroyed by John and his son, Basil. Three years of this strategy was taking its toll on John's popularity. Eudokia wasn't happy that John wasn't spending time with her or their children. The nobles and peasants were angry that their lands were being burned and pillaged. The Armenians in particular had to be held in place in order to ensure the strategy's success. Finally, John and Tughril, both tired from the war, agree to a truce. Tughril had been asked by the Abbasid Caliph Al-Qa'im to expel the Shiite Buyids from Mesopotamia, and there were rumblings of discontent in his own family back in Khorasan.
1051-1054 AD:
John kept his end of the truce. He would need to for his rebuilding program to take place. It was no small task - refugees and Turkish converts would have to be relocated, fortresses, towns and cities would need to be built and rebuilt, with some help from Norman engineers. John, seeing no choice, raised taxes on the peasantry, but only slightly. The nobility bore still bore the brunt of his laws, and their discontent finally boiled over into a rebellion in Phyrigia by Gregory Taronites in 1052 AD. George Maniakes was sent against the rebels, but when he arrived, Gregory had already been killed by his soldiers who swore proclaimed him emperor instead. George Maniakes, now feeling ignored by the emperor and upset at the tax increase, readily agreed. The rebel army marched towards Constantinople but was halted at Nicomedia by Isaac Komnenos and Nikephoros Bryennios. During the battle, George Maniakes was killed after receiving a fatal wound in battle. Without a leader, the rebellion collapsed. John mourned Maniakes' senseless death. As a reward, John made Isaac the new Catepan of Italy.
In 1054, the aging emperor agreed to marry Basil to a daughter of Bagrat IV of Georgia, even though Basil had fallen in love with the daughter of a Crimean Goth. As it turned out, when the Georgian princess arrived, she was 15 turning 16, more Alexander's age than Basil, who was 28 years old. Furthermore, she wasn't even Bagrat's daughter, but a member of a family branch in Alania. Taking pity on the girl, who was renamed Eirene, and seeing Alexander's infatuation with her, married them instead and allowed basil to marry the Gothic girl. John still worried for the future of the realm he and his father had worked so hard to protect. He had feared there would be animosity between Basil and his half-siblings, but surprisingly, they got on very well, as if they were born to the same mother. Still John worried. At one point he turned to a mystic for help, who gave him an 'answer':
"Why seek the future when it is the past that you need?"
John pondered what this meant. After going through the great library, he realised what he and his sons would have to do - Four hundred years ago, a single loss at Yarmouk had opened Syria, Palestine, Egypt and North Africa to the first followers of the Prophet. But there were still Christians in those lands, and if the Romans played their cards right, those lands could be forever liberated from the Mohammedans. The time would come soon. The Fatimid Caliphs of Cairo were losing more power to their viziers, and though they had briefly taken Baghdad, the tribes that had bore the brunt of the fighting - the Banu Hilal and Banu Sulaym * - were nearly wiped out by the main Seljuk/Abbasid army. John personally took charge of his sons' education, seeing in them the best and brightest hope for restoring the empire of Justinian and Maurice.
Finally, Patriarch Michael Cerularius received a letter from the Pope Leo IX in Rome, which proclaimed his position as rightful head of all Christianity, citing the Donation of Constantine as proof. Michael outright refused the claim, while John personally sent correspondence to Rome, diplomatically telling the Pope to "reconsider the time and place for such a discussion or else I will come to Rome myself and 'donate' the 'Donatio' in whatever orifice I believe suitable at the time." Despite Leo's death, the letters are taken as a threat of attack against the Papacy itself, and a Latin cardinal nails a bull of excommunication. Patriarch Michael threatens to excommunicate the Bishop of Rome in turn, but John holds him in check. Legally, the bull means nothing due to Leo's death, so John politely requests the Patriarch discuss the matter no further, or else he will make him well and truly celibate...
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*: IOTL the Fatimids sent them against the Zirids in North Africa, where they caused untold damage to the agriculture of the region.
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Children of John II Makedon:
Basil - Theodora of Gothia
Agatha - Nikephoros Diogenes
Alexander - Eirene of Alania
Leo
Stephen - betrothed to Maria Komnenos