She agreed to be under his chain of command.

Once Samus agrees to follow his orders, then yes, he can order her around.

Even if Samus does have top-level clearance, she has no 'Need To Know' what is going on at the Bottleship. You also have to have a 'Need To Know' the Top Secret information.

People with 'Top Secret' clearance are still not allowed to read the vast majority of Top Secret files. That isn't how security clearance works.And how does Adam know what her clearance is? How does he want her to work with them without telling her what's going on? She should already have one of the highest security clearances available. The Marines work with Samus just fine in Prime 3. He says he needs to ask her to work with them and follow his orders. Then Adam can order her off the station, or arrest her.Even if Samus had that kind of pull, it takes forever to get that sort of thing done even if you're not talking about a secret project like breeding Metroids. We'll get back to you as soon as we can.' Seriously, people, bureaucracy. We'll see about getting your security clearance at our next meeting, taking place in two weeks, after which we'll have to form a committee to study the feasibility of giving an independent bounty hunter authority over our duly promoted and designated officers. 'Hello, Samus, this is the senator for your quadrant.'Hello? Senate? This is Samus Aran, Galactic Hero calling.Besides, almost the first words out of his mouth were that she was an outsider, and therefore not cleared to know why he was there, which kind of precludes any further discussion on the matter. She knew he must have his reasons for being there.

Why didn't Samus press Adam for a reason why he was there? A General showing up is really, really suspicious for a simple SOS response.

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