Just like it was said, 5 days later, Link woke up from the Shrine of Resurrection and was unprepared for what was to come as soon as he ran out of the door.
He was stunned when out of nowhere, an old man punched him and knocked him unconscious. However, it was not an old man that had knocked out the freshly revived Hero, it was a Yiga Clan member in disguise.
In the distance, the real old man hollered, trying to stop the attackers, but to no avail. The duo of Yiga soldiers had teleported away from the scene of the crime, and the spirit could not chase after them, for he was trapped on the Great Plateau for all of eternity until the Calamity would have been defeated, and without Link, that task would never be completed.
After the two Yiga soldiers laid an unconscious Link on a spare bed in the Yiga Clan hideout, the entire group abandoned from their disguised positions throughout Hyrule and returned to their leader. Now was the hardest part of the mission. Coming up with a story and sticking to it.
The two soldiers who knocked out the Hylian made sure that they were well disguised to the point where you could not spot a difference. They had done that for two reasons. The first being that, once awakened, the Hylian would not listen to the old man and the second being that because they were disguised, the boy would have no idea that it was the Yiga Clan that had knocked him out in the first place.
The group had to come up with a story, and every single member had to stick with it, no matter what. After several ideas were thrown about, the final story was made. It was also decided that they would come up for a new name for the Hylian, therefore, if anyone ever mentioned his name, he would have no idea that the person who mentioned his name actually was referring to him.
Their final story was this: Sheik, the name decided on for Link, had been fighting against several people who opposed their Lord Ganon, when one of the attackers had wounded him severely. The last person had also died from their wounds and the leader of the Yiga Clan from that time, Master Taho, had him rushed to the Ressurection shrine before it was too late.
He had been in the shrine for 100 years, and they were about to show him back to his home, but a descendant of the attacker who had killed him, attacked the hero when he was still unsure about anything. The attacker was secretly disguised as an old man, but really wasn't, and he ran off before he could be stopped, and took shelter at Kakariko Village.
They would attack the village to kill his 'attacker' once Sheik was all better and retrained in the ways of the Yiga. If he knew nothing, he would be quicker to learn the ways of their tribe.
Satisfied with their story, and discussing some of the small details to make sure that everyone understood it, everyone had to recite the whole story multiple times to make sure that everyone understood it and memorized it.
They all now had to wait for their newest member to wake up from his second slumber, and everyone was nervous. The members of the Yiga and also talked to the Calamity using signals, basically telling the Calamity that the once-threatening Hero, was now a member of their group and that he was no longer going to be a threat.
The entire clan knew that they would not be able to defeat the Hylian Champion, but having him join the clan would make them stronger, to the point of being unbeatable, ever. Hyrule would soon be taken over by the Yiga Clan, but they would have to wait for the perfect moment.
Unknowing to them all, Zelda had learned the signs the Yiga had learned to communicate with Ganon, and she found out the information. She had to warn her hero quickly, before it was too late for everyone.