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Let's say hypothetically that lower courts en masse decide to ignore Supreme Court decisions.
The alternative is the same whether just one lower court or many lower courts ignore SCOTUS precedent. An aggrieved parts will appeal the lower court ruling, and the matter will work its way up the ladder until SCOTUS directly rules on this application of the law. This sort of happens all the time, when lower courts don't apply the ostensive "final ruling" because they find that there is some other overriding consideration ("that rule only applies to businesses employing more than 50 people").
Where the case to be remanded to lower courts for further proceedings consistent with SCOTUS opinion and still the lower courts refuse to comply, i.e open rebellion, SCOTUS could rule that non-compliance by lower courts constitutes contempt, and an order could be issued for the removal (in some form) of offending parties (we may presume, the justices of the lower court). The statute outlining court power allows on order of imprisonment for "disobedience or resistance to its lawful writ, process, order, rule, decree, or command". Federal marshals would then arrest non-compliant judges, unless the marshals too are in open rebellion. If the judges in question were federal judges, the marshals would have to decide whether to obey the order of SCOTUS vs. the order of the district or circuit court. Since under the US Constitution states that "The judicial Power of the United States, shall be vested in one supreme Court, and in such inferior Courts as the Congress may from time to time ordain and establish", it is objectively established that SCOTUS rulings are superior, so provided that the marshals elect to uphold their oath of office, they will enforce the SCOTUS ruling. However, citizen action becomes irrelevant once SCOTUS has made its ruling, and the matter has moved from legal determination of fact to enforcement of established fact.
While an appellate court may have the opportunity to reverse any individual trial judge every few years, I know that trial judges, in their numerous workday rulings, reverse appellate courts every day.
Lets say hypothetically that lower courts en masse decide to ignore Supreme Court decisions.
What legal alternatives are available to citizens if lower courts "Go rogue" and decides to ignore a Supreme Court precedent?
Appeal is one option and if the violation is blatant, a swift per curiam bench slap is sometimes employed. See, e.g:
James v. City of Boise, 15-493, challenged the Idaho Supreme Court’s, um, idiosyncratic view that when the Supreme Court construes federal law, it “does not have authority to limit the discretion of state courts where such limitation is not contained in the statute.” In just one-and-a-half pages (more than one-tenth of which consisted of a single quote from the Court’s 1816 decision in Martin v. Hunter’s Lessee) the Court clarified that “[t]he Idaho Supreme Court, like any other state or federal court, is bound by this Court’s interpretation of federal law.” Some have speculated that this case is a shot across the bow of the Alabama Supreme Court. The implications of James will become clearer in the future, once we know what has actually happened.
Is there any punishment higher courts can hand down to lower courts for ignoring their decisions?
Not really. But, a judicial discipline body in state court systems sometimes intervenes. Former Alabama Supreme Court Justice Roy Moore, now a U.S. Senate candidate, was removed from office twice (he was re-elected in between) for defying clear U.S. Supreme Court precedents openly.
Also, the ACLU in both Mississippi and Colorado amassed convincing evidence of flagrant and widespread instances where municipal judges, who are more subject to political authority, were routinely disregarding the law in the past year. Both resigned with the attention and in the Mississippi case the municipal court involved was actually abolished entirely.
Injunctions from federal courts aimed at civil rights violating practices in the court system (e.g. not releasing people free on bond pending trial for non-payment of an administration fee, or repeat mistaken identity arrests not brought promptly to court attention) usually target the law enforcement or prosecuting attorneys' involvement in asking for the relief, rather than the court itself.
