In the end the mandate stands because it is a tax not a penalty and the federal government can't withhold all medicaid money from states if they don't expand who they cover under medicaid. But that one problem can be severed from the rest of the act, so the rest of it stays. Ginsburg, Kagan, Sotomayor and Breyer would have found the mandate - whether penalty or tax - was fine under the commerce clause. Scalia, Alito, Thomas, and Kennedy think the whole law was bogus and would have killed it. It's a long, but ultimately not that complex, decision. The ramifications? Anyone's guess except that everyone will be in the healthcare pool now, which is a boon to insurers and, hopefully, ultimately leads to a reduction in costs. But knowing insurance companies, that's doubtful.
Below is a complete analysis of the opinion from my legal perspective.
Anti-Injunction Act does not prohibit review because Congress did not label individual mandate as a tax. Both the healthcare act and the anti-injunction act are laws passed by congress, so the Court must assume the words were chosen carefully. The mandate is penalty, not a tax. This creates a pickle for Roberts that becomes relevant later.
Commerce clause doesn't allow individual mandate because Congress can only regulate activity. It can't regulate inactivity. This holding sets precedent that Congress cannot use the Commerce Clause to "compel" economic activity. Roberts goes after Ginsburg's concurrence and the cases she sites, saying that all of her cases included either an activity (as opposed to inactivity) or were not Commerce Clause cases.
Roberts adopts the "government can't make you eat vegetables" argument. I still don't buy it.
Roberts saves the individual mandate by finding it actually operates as a tax even though it's labeled a penalty. Significantly, the reason Roberts goes this route is because part of the Court's job is to try to find a law constitutional. The Court's job is not to try to find things unconstitutional. Basic rules of statutory reading require the Court to uphold a law when it can, even if that means reading a statute in a way that might not be obvious. This is the key part of the opinion and is the reason why the individual mandate (and likely the rest of the law) is saved.
This tells me Roberts does care about his legacy and the legitimacy of the court. But this is actually an easy save for him to make. Like I said, it's a basic rule of statutory construction - the Court must look for ways for a law to be upheld. This is not revolutionary or even difficult/complex. It's Constitutional Law 101 stuff.
The slickest part of Roberts' opinion is finding first that the "penalty" label of the individual mandate means that the Anti-Injunction Act doesn't apply and then (a few pages later) finding that the label of "penalty" does not determine constitutionality. This is where critics will focus (IMHO). But it's not really an issue. Labels (i.e., how Congress names something) matter when applying the Anti-Injunction Act, but they don't in determining constitutionality. The reason is in part three of my summary - a Court must try to save a law, not strike it down.
You might be asking, if Congress can't regulate inactivity via the Commerce Clause how can it regulate inactivity via the taxing power? Good question. Roberts answers. Regulating inactivity via the Commerce Clause is not an enumerated power in the Constitution. Taxing is an enumerated power. Thus, Congress can tax but the tax must not - ironically enough - be a penalty. In other words, the tax can't be a surreptitious regulation. Here, the fine for not having healthcare is, in effect, a tax. It's collected by the IRS, but, and this is key, the IRS can't punish you criminally for not having healthcare. Thus, though the tax is designed to influence behavior, it does not compel behavior. You always have a choice not to buy insurance and if that's your choice, you simply pay an additional tax.
The other issue was whether the expansion of Medicaid was o.k. The Court found that Medicaid could be expanded, but the Federal Government cannot withhold all medicaid funding from the states if the states don't agree to expand medicaid. Medicaid previously just covered some people - seniors, poor people with kids, disabled, and blind people. The new law expands it to include all poor people. So, the program can be expanded, but states cannot be penalized for not agreeing to expand their state programs. The government can persuade, but not compel the states to expand. Persuading would be offering some incentives or withholding some funding if the states didn't expand. But the law allows the government to withhold all medicaid funds from states - even the funds for persons traditionally covered by medicaid. That's unconstitutional. But that provision can be severed from the rest of the law, so the rest of the law stands.
Ginsberg thinks the Commerce Clause allows for the individual mandate. She examines the history of the clause, quoting the Constitutional Convention, which found that the clause allowed for laws to regulate economic interests "in all Cases for the general Interests of the Union, and also in those Cases to which the States are separately incompetent." I guess this wasn't persuasive to those two "originalists" Scalia and Thomas. She gives a good history of states' efforts to solve the healthcare problem, showing they are incompetent to solve the problem.
Ginsburg rejects Roberts' argument that those who don't purchase insurance are not "active" in the health care market. She cites statistics that 60% of non-purchases actually visit a Dr. or hospital each year and 90% do so w/in 5 years. She also notes that Congress has the power to define a market, not the Court. Congress defined the market as those who are using or will use health care. Roberts re-defines it as only those currently using health care. She also addresses the forced-to-buy-vegetables argument by noting that everyone will use health care at some point, not everyone will eat broccoli. Also, if you do eventually want broccoli, you have to pay for it. Here, you will eventually want healthcare, so you have to pay for it now.
A central theme for Ginsburg is that the healthcare market is unique. Everyone will get healthcare at some point and, right now, those that don't buy insurance get it for free burdening the rest of those that do. No other market is like that. Yes, everyone buys food, but those that need food don't get it for free thereby increasing the costs on everyone who does buy it.
Ginsburg disagrees with striking down the medicaid penalty provision. In essence, she says that Medicaid is the perfect example of cooperative federalism and that the federal government can and does provide the funds to the states for the programs. If the government could, tomorrow, completely eliminate funding for medicaid or eliminate the program altogether, it can use those funds to encourage states to expand their medicaid programs. That the states really need the federal government's money to support their state-based medicaid program is the essence of the Spending Clause. The fed. gov't gets to spend its money.
Scalia, Alito, Kennedy and Thomas start their dissent decrying the "Court's" expansion of the commerce clause and laments the fact that we now have a dept. of education, a dept. of housing, etc., none of which are in the text of the Const. So you know where they're going. But they ignore Ginsburg's citation to the constitutional convention regarding the purpose of the commerce clause. Funny, that. The precedent the justices cite for striking down power exercised under the Commerce Clause is all either from the Rhenquist or Roberts court. That seems to me to say that those two courts have a - putting it lightly - different view of the Commerce Clause than the courts from the previous 200 years. Funny, that.
The dissent disagrees the individual mandate is a tax because the act doesn't say it's a tax, it says it's a penalty. Because the language of the act is important, the dissent that it is "unavoidable" that they mandate is a penalty and not a tax. Because it is unavoidable, the mandate cannot be saved. Regarding the medicaid expansion, the dissent agrees with Roberts that the threat of withdrawing all medicaid funds from states that don't expand their program is coercion and thus unconstitutional.