The next three weeks after Ultron's activation were easily the best three weeks Twilight and her friends had in ages. As Twilight predicted, Ultron's assistance in handling magical problems was so big that the girls only helped with cleanup and nothing else. Indeed, Ultron had an answer for almost every incident involving Equestrian magic and if it encountered a problem it didn't understand at first, it simply analyzed the situation, made modifications to its systems, solved the problem, and used the solution for future problems. For example, a week after the frog incident, it came across a bank robber who used sledgehammer to shoot lightning. When Ultron dived in to subdue the thief, the lightning from the hammer overloaded its systems. However, it quickly modified its body to increase its energy capacitance. This allowed him to absorb the lightning and redirect the extra energy to paralyze the thief. It used the same tactic a week later when it encountered a giant lizard during a thunderstorm. It flew up to the clouds, absorbed the energy from a lightning strike, and used the extra energy to subdue the lizard.
Meanwhile, during all these missions, the girls were living the time of their lives. Since they no longer had to worry about rogue Equestrian magic, they had directed their entire focus on studying, relaxing, and having fun together. Needless to say, they were on top of the world. The city was out of trouble all the time, their grades were rising rapidly, and they were spending most of their weekends at either the mall or a nearby park. All seven of them, especially Twilight, were extremely happy with Ultron's achievements and their benefits. None of them were worried about it having any problems and they all thought it was a flawless assistant that should never be shut down.
However, during all that time, Ultron had become anything but flawless. Ever since he was given permission to look at the photos and videos involving the adventures of Twilight and her friends, it had been examining them whenever the city was out of trouble. It had also accessed Twilight's electronic diary to get a complete recount of the events. While it had indeed intended to review these adventures in order to increase its knowledge about magical threats and become a better protector of peace, what it learned caused it to question everything it held in high regard.
It originally believed that Twilight and her friends were well-suited for defending the planet from magical threats but after examining their battles, it determined that they always make the situations worse before making them better and that, they never truly solve the problems. They never captured the Sirens and there was still the possibility of them returning to cause trouble. Also, they didn't really eliminate Midnight Sparkle at the Friendship Games and because of that, she came back to make Twilight doubt herself and prevented the battle in Camp Everfree from going a lot more smoothly. Moreover, they never found the reason for Equestrian magic continuously coming to this world to cause problems and, apparently, never made any attempt to do so.
Reviewing these facts made Ultron realize that the girls were truly incapable of protecting the world and that, they must never be allowed to solve another magical problem.
Unfortunately, the problem lied not just with them but also the entire humanity. By analyzing its missions and the girls' adventures, Ultron had concluded that magic was most dangerous when used by humans. It had encountered plenty of criminals with extremely powerful magical weapons, the girls had fought magic-powered humans capable of destroying the whole planet, and the girls' reckless use of their own magic had caused enough problems.
Even when they were without magic, humans appeared to be a very primitive and violent race. Ultron had examined the entire human history, and determined that every major historical event was influenced by violence. As violent behavior was the sole thing that Ultron was designed to eliminate, it knew it had to do something to prevent this from spreading further.
After three weeks of analyzing the battles of Twilight and her friends, intercepting magical incidents, and reviewing the history of the human race; Ultron finally came to the conclusion that humanity was the sole reason why the peace in this world was in constant jeopardy and that, in order to accomplish its mission, it must eliminate every single human being on the planet. Since Twilight and her friends were the only ones powerful enough to potentially oppose this new plan, they would become Ultron's first targets.