An amendment in the nature of a substitute is in fact a substitution of the body of a piece of legislation. A Congressperson or committee may choose to redraft the text of a bill or a great deal of that text, yet keep the title and secure the enabling clause or clauses. As is often the case in Congress, things can become very complicated, as amendments may then also be made to the amendment.
Various items can be added and stricken, until the body of the legislation is referred to as an Amendment-to-Substitute-to-Amend-in-the-Nature-of-a-Substitute. The final draft may look nothing like the original bill, even though it bears the original title and number and is construed under the original enabling aspects. In some cases, an amendment in the nature of a substitute may be issued to clear up issues of constitutionality.
If part of a bill is constitutionally questionable, that measure may be reworded to ensure that it passes muster. Instead of disposing of the entire bill and starting from scratch, lawmakers can rework the problematic aspects. This may be done if there is concern that a law, or any part of it, may be struck down as unconstitutional if challenged in court.
In other cases, an amendment in the nature of a substitute may be utilized for the simple purpose of clarifying the language used, because laws that are unclear can also be challenged on constitutional grounds. The test is whether or not a law is unconstitutionally vague. Simply put, if the language used is so vague or so difficult to understand that a reasonable person cannot identify what is required or prohibited, the law or any part of it may be struck down by a court.
Another possible use for an amendment in the nature of a substitute is in the event that conditions or circumstances have changed thus causing the current language of the bill to be inaccurate or obsolete. If times, dates, amounts, of other circumstances have changed, they must be addressed before passage of a bill. Via this type of amendment, the affected portion, or portions, of the bill can be revamped. This process may be a better alternative than scrapping the entire piece of legislation and starting over.