Tony Stark, also known as Iron Man, was facing a dilemma: Pepper was away, both for work and to have a closer look at the magical school that had seemed most promising when they had looked into the information, and he was supposed to look after Harry, having been told that 11 or 12 year old boys should not be left alone for long periods of time, he might be perfectly capable of looking after himself, but might need the help of a responsible adult, and if one wasn't present Tony might do, as he was at least adult, and Harry was still too young to imitate (most of) his most irresponsible behaviour, and boys were allowed to do some things that were frowned upon when an adult did them. Anyway, the problem was that Nick Fury, the director of SHIELD, had asked for his assistance, and made it clear that it was actually an order, and he couldn't refuse it, so he could either leave Harry alone for a while at Stark Tower, risking Pepper's Wrath, or he could take him with him, which would irritate Fury. It didn't take him long to decide: Fury might have more influence, but he was honest enough to admit, if only to himself, that he would be in far worse trouble if Pepper was angry at him, as he still depended on her for several things, and she could make his life really miserable if she wanted to. Besides, how much trouble could Harry get into coming with him? Certainly less than by staying at Stark Tower, last time he had been left unsupervised in one of the labs only the timely intervention of You had prevented a serious fire, after he shortcircuited a new, experimental machine that shouldn't even be able to do so.
Fury was less than thrilled about Stark's little tagalong, but didn't bother to protest too much, he just got one of his agents to show Harry to a room, explain where the cafeteria was, and make sure he understood that he was not allowed to wander around on the helicarrier, going anywhere but the places he had been showed, and it would be best if he didn't move from his room at all, to which Harry reacted by promising that he had no intention to do anything but playing with his videogame, omitting to mention that the game consolle had been heavily modified by Tony, and he didn't exactly intend to play with any of his 'videogames', having his consolle hacking into the videocameras on board the helicarrier for fun could be considered playing too, couldn't it?
An hour later, a very aggravated Phil Coulson went to confiscate Harry's videogame, and tell him that hacking into the network of an agency such as SHIELD, even if only the cameras, could be considered a crime, then he went to Tony, to berate him for letting Harry play with such a piece of equipment. Now bored, Harry went to the cafeteria, and proceeded to make the most out of his unsupervised time with the snack machines, until an agent arrived and asked if he hadn't eaten enough sweets already, then he went to explore the flying ship.
By the time the alarms sounded, Harry's sugar rush was over, and he had managed to get lost, so he was relieved to see Coulson, even if the agent was in a hurry to check on Loki. Coulson was not going to leave a child wandering around on his own on the helicarrier during an emergency, but unlike Stark, there were several things he feared more than an angry Pepper, and so he just told Harry to follow him for now. When Loki attacked him with his staff Harry was right behind him, and scared enough for his accidental magic to kick in, creating a spherical shield which lessened the blow considerably before giving out, leaving Harry unharmed but dazed, and Coulson injured, not critically but enought to prevent him from stopping Loki. Coulson dismissed the sphere as some new technology, while Loki recognized it for what it was, but didn't bother to do anything about such a young, untrained magic user. While Coulson went to the nearest infirmary to get patched up, Harry wandered off again. As the helicarrier shook he realized that perhaps it hadn't been such a good idea to go exploring, after all, a conclusion that was only reinforced when he hit his head against a wall. The people around were all busy, so he found an office and decided to wait there until it was all over.