He could face legal issues within the wizarding world. There are likely laws against using magic to control others without their consent. So, he might find himself in front of the Wizengamot, facing serious charges. This would not only damage his reputation but also put his future at Hogwarts and in the wizarding community in jeopardy.
One consequence could be that he loses the trust of his friends. They might be afraid that he could control them at any time.
One challenge could be controlling the intensity. Lightning is extremely powerful, and if he doesn't have proper control, he might end up causing more harm than good. Another might be the unpredictability of the element itself. Lightning doesn't always behave as expected in nature, and it could be even more difficult to manage magically. Also, he may face opposition from those who fear his power or think he's becoming too powerful.
One consequence could be that it makes him a more formidable opponent. His enemies would have to rethink their strategies as he can now teleport.
One consequence could be that the wizarding world starts to view him with even more suspicion and fear. People are already afraid of dementors, and if Harry can control them, they might think he's becoming too powerful or even turning to the dark side.
Maybe it could be through some kind of magical accident. For example, he might have stumbled upon an ancient spell during one of his adventures in the Forbidden Forest. Or perhaps it was a latent power within him that was awakened by a powerful magical artifact he came in contact with.
Well, it could change the whole dynamic. He might use it to manipulate enemies, like making Voldemort's followers turn on him. This would speed up the end of the war perhaps.
On the positive side, he can use it to protect Hogwarts. He could be like a living, breathing firewall against any fire - related attacks on the school. For instance, if the Dark Lord tries to set the castle ablaze, Harry can use his fire - controlling ability to counteract the flames and keep the students safe.
In some fanfictions, it could be due to a new jutsu he discovers. Maybe during a secret training session in an ancient scroll, he finds a forbidden technique that allows him to control people.
He might also face moral dilemmas. For instance, using this power to heal someone might seem noble, but if he uses it to harm or manipulate others, it would be a different story. He has to constantly struggle with the right way to use this power.
One possible consequence could be a moral breakdown within Harry himself. He's always been against dark magic, so using Crucio might make him question his own values. Another consequence could be alienation from his friends and allies. They would likely be shocked and appalled that he resorted to such a cruel curse.