Section 3 deals with the federal government's refusal to recognize same-sex marriage. Section 2 grants states the right to refuse to recognize these marriages. Section 1 is the title and definition part.
Edith Windsor challenged the federal government's decision to charge her $326,000 for estate taxes on her late spouse's estate. Had her spouse been a man there would be no estate tax due because spouses can transfer an unlimited amount of assets between themselves. Windsor's case argues that her marriage was legal in both Canada--where she and Thea were married--and in New York where they lived. Both jurisdictions recognized the marriage. Under DOMA, however, the IRS was prohibited from doing the same.
Windsor is not challenging DOMA as a whole. This is an incremental step in the process.
If Windsor is successful, the Supreme Court will declare Section 3 unconstitutional as it is applied in marriage equality jurisdictions. That includes 12 states (Massachussetts, Maine, Vermont, New Hampshire, Connecticut, Rhode Island, Delaware, Maryland New York, Minnesota, Iowa and Washington) and the District of Columbia.
It will NOT apply in the 28 remaining nonrecognition states. It MAY NOT apply in the states that permit some type of recognition like Civil Unions or Domestic Partnerships (California, New Jersey, Oregon, Colorado, Hawaii, Illinois and Wisconsin). California
But, no one knows exactly what will happen until the Court issues its decision--and that will come next week. The Court's session ends at the end of June.