Apparently this scene didn't happen enough
As clashes with the Spanish increased alongside his concerns over succession Atahualpa faced a multitude of problems, some of which he saw and some of which he did know. One thing that was in his favor was Sebastián de Belalcázar. The old conquistador still ruled in San Miguel, and his control of the city was undisputed, though Belalcázar did not particularly care about the raids done by fellow Spanish he did keep trade flowing into the empire from Spain. Any full on invasion would have cut into his profits and so he cracked down hard on any attempts at invasion. But the increased strain on relations was cutting in on his profits, and he faced increased suspicion at home. Many Spaniards could not comprehend that skirmishing was in fact an upgrade in violence instead of a deescalation of hostilities. Rumors began to swirl about Belalcázar's position. Rumors began to swirl about his relationship the the heathen natives. Rumors began to swirl that he was being payed off to keep the peace. This was, of course, completely and utterly true. Belalcázar had indeed been given large amounts of precious metals to stop his invasion of the empire. But these rumors expanded into a vast conspiracy headed by Belalcázar to keep other Spanish from raiding the Tawantinsuyu and to turn over Spaniards to the pagans for "vile rituals". These were slightly less true. Belalcázar did try and keep some raids from occurring, fearing retaliation against San Miguel, but if he himself profited he backed them. And when Spaniards found themselves seized by the Empire and pressed into the service of the Sapa Inka official protests often faded if Atahualpa poured a bit more silver into that month's purchases of gunpowder. Rumors that Belalcázar had abandoned Catholicism and had embraced the "pagan sun cult" of the natives were completely false.
Into this cesspit of rumors and half-truths waltzed Juan de Carvajal[1]. Not much is known about Carvajal earlier exploits, but sources from before 1545 have him hopping around Central America and the Caribbean. Like a few other brave souls before him he arrived in San Miguel determined to ignore Belalcázar and launch a full on invasion of the Tawantinsuyu empire. Unlike previous such men he came with a few hundred men, all ready to take on the Tawantinsuyu the minute they arrived on March 16 1545. Belalcázar balked and began his usual habit of denying supplies towards troublemakers. In response Carvajal made preparations to leave immediately. Skirmishes ensued between Carvajal's men and Belalcázar's men, skirmishes that began to turn out dangerously well for Carvajal. In response Belalcázar played one last card, a move that is hotly debated to this day. He sent a message to Quisquis in Tumbez.
Despite what some may say it was not a plea for help. It was not an invitation to enter San Miguel to crush Carvajal. It was a statement in his capacity as "Captain-General of Nuevo Oaxaca" that Carvajal was not a merchant "but a bandit" who by being so "forfeited all protections given to him by god and the law". The message was clear, Belalcázar would not raise a protest if Carvajal was crushed by Quisquis. Belalcázar was panicked about the loss of wealth that he would incur should Carvajal succeed. Belalcázar was also panicked about a loss of wealth should Carvajal be defeated and the Tawantinsuyu retaliated my storming San Miguel. Fragmented reports show the Quisquis was confused by the message and suspected a trap, and so sent out only a fraction of his forces, mostly crossbow men and only a few horses. They lay in wait just a few miles outside San Miguel to ambush Carvajal. On April 12 they attacked Carvajal's force as it marched towards Tumbez. But Carvajal had the benefit of hindsight and was well prepared for such an attack. And so, unlike previous Conquistadores, his men formed up, stood firm, and drove back the attacking party. Carvajal demonstrated clearly that while the Tawantinsuyu were quickly adapting European weapons they still lacked a firm grasp of the tactics needed to utilize them perfectly.
Carvajal's tactical superiority would prove less useful when he reached Tumbez. The city, as was custom, ridden by plagues and food supply issues. However here Quisquis had a massive numerical advantage and the most formidable native built defenses in the Americas. Had Carvajal been better acquainted with the politics of the area he might have around Tumbez and rallied angry anti-Tawantinsuyu locals. But by attacking early he had only his own men to rely on. He didn't have the numbers for a siege nor the strength to take the city. 4 times he tried to gain entry to Tumbez, and he failed 4 times. His strength dwindled, and it became apparent that he faced death or capture. So Carvajal took his remaining men and returned to San Miguel on April 29 and sailed back off towards Panama.
Angered by the interference of Belalcázar Carvajal intended to take up his grievances with the Real Audiencia of Panama[2], which had nominal legal authority over San Miguel, though this authority had never been tested. However he found little restitution in Panama City. San Miguel kept Panama City an important place for merchants or would be bandits to travel through as they went to and from the Tawantinsuyu Empire. All of the Audiencia members had their fingers in the pie and also were receiving bribes that Carvajal could not hope to match. So Carvajal traveled even further north into lands conquered by Cortes.
There he appealed to Antonio de Mendoza, Viceroy of New Spain. The role of San Miguel had always been somewhat ambiguous, having come into existence by a Treaty with a foreign power. This meant who exactly had final say over it was in dispute. Mendoza went for the chance to assert control over San Miguel. He sent a message south demanding the Belalcázar come to Mexico City and a point for the story Carvajal was telling, which by now included human sacrifice. Instead he got a letter denying the allegations, asserting that nowhere in the founding documents of New Spain or Nuevo Oaxaca was the Viceroy of New Spain given any authority to pass judgment on the Captain-General of Nuevo Oaxaca. Mendoza responded with a further demand for Belalcázar to come to Mexico along with a formal judgement that Carvajal receive compensation for his losses. Belalcázar responded by sending a subordinate to Mexico who reiterated the previous point about lack of jurisdiction while also pointing out that judicial matters such as this were typically handled by Audiencias. Mendoza had had enough and formally declared Belalcázar outside of the law and stripped of his titles. Carvajal was giddy.
Then Mendoza did nothing.
See Some Evil, Hear Some Evil, Send Strongly Worded letters to the Evil
Antonio de Mendoza was a cautious man by nature, and had larger issues then a rebellious conquistador for to his south. Indeed had Belalcázar not been so spectacularly insubordinate it is unlikely Mendoza would have done as he did. Mendoza was a man who would advise his successor in New Spain to "Do Nothing, and Do it Slowly". When it came to organizing anything to force Belalcázar out of San Miguel Mendoza offered no help outside of declarations in his capacity of Viceroy. And that proved little help to Carvajal in Mexico, where local Spanish landowners resented attempts to expand the crown's power. Thus they were not supportive of a man whose sole claims were the dubious declarations of the Viceroy.
Carvajal might have been planning on giving up then and there, maybe galavanting off to Venezuela or something. Or perhaps he indented to sail across the Atlantic and press his claim with the Council of the Indies. But as he prepared to leave Mexico City he was hit with a bout of fever that kept him bedridden for months before killing him on January 4th 1546. Carvajal's rather anticlimactic death also killed off any chance of a private venture removing Belalcázar. From now on it would almost certainly being the Spanish crown enforcing Mendoza's decisions if they were ever actually enforced. Ironically it was around the time of Carvajal's death that Charles V and the Council of the Indies began to look at Mendoza's dispatch attacking Belalcázar's conduct.
Meanwhile Belalcázar responded to news of his removal with several actions. He beefed up the defenses of San Miguel, turning cannons towards the sea and raising the walls. No one seems to have informed the Tawantinsuyu of the change, which is odd. Obviously Belalcázar was not keen on telling them that he no longer had the backing of the crown, but generally the Tawantinsuyu were kept fairly well informed about events in San Miguel via spies, bribes, and captured Spaniards. It is possible they did hear rumors of the incident but dismissed them for some unknown reason. In any event these rumors, and Belalcázar's fortifications, slowed when word arrived of Carvajal's death.
So Atahualpa continued raising his sons and pursuing modernization. All the while the situation was shifting outside of his control, not just in San Miguel but also in Klein-Venedig.
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1: Best known IOTL for violently ending the Welser's experiment in German colonialism.
2: IOTL a combination of corruption and Pizzaro's conquest meant that it would split up into two Audiencias, one in Lima and the other in Guatemala City. With no vast new conquest to govern it remains, though still very corrupt.