What do you mean by effectively challenge the government? Corporations challenge the government all the time. The power of the government is constrained by the constitution, and corporations have been recognized as having certain rights. The government does have the nuclear option though. Alphabet only exists because it was granted a corporate charter by the government in whatever state they incorporated in. The state can revoke its charter and the government can force them to liquidate their assets. It used to be a fairly common practice and still happens quite a bit too smaller corporations.

What I mean is how big does an organisation have to get to effectively challenge the sovereignty of the government. How big does it have to get (relative to the government size) that (threatening to or actually) revoking its charter won't mean anything because so many people are tied up in the corporation that it can just exert its own authority.

I.e. Is there a theoretical size in which the corporation (or effectively any other organisation) can just say "no" to the government?

I don't think any company of any size could just say no. No corporation has enough power to stand up to the government if the government is determined. They do have a lot of soft power to keep things from getting to that point. They can spend a lot of money to influence politicians and the public and apply pressure to the government to back down. Walmart, for example, has ~2.2 million employees. Even if Walmart did something egregious enough to have their charter revoked would you want to be the governor of the state that has to tell those 2.2 million people they don't have jobs tomorrow? Not to mention the enormous ripple effects that would have through the economy. I've seen a lot of people argue that what the banks did during the lead up to the financial crisis was egregious enough to warrant the corporate death penalty, but those institutions were so critical to the economy that they couldn't be shut down. So, in a sense, there are already quite a few companies that are too large for the government to effectively exercise it's power over.

I don't think there is a set number though. It probably depends a lot more on what the business does and how central it is to the health of the economy. It's the "too big to fail" debate, and at various times in the recent past, we have determined several automakers and financial institutions to fall into that category. I think if you are too big for the government to let you fail, you are too big for the government to try to shut you down.