Something is missing from this story. According to the article, they started to process of trying to get legalization about 13 years ago, but he only faced a removal order about 9 years ago. He also would have normally been granted citizenship through marriage with his wife.
Whether the immigrant can "adjust status" -- that is, apply for a green card without leaving the United States -- depends on whether he or she fits into one of a few narrow exceptions. The immigrant can adjust status only if he or she either:
legally entered the U.S. with a visa or after inspection by an immigration officer (and wasn't just using the visa with the intention of applying for a green card based on marriage, which happens to be visa fraud) and is either marrying a U.S. citizen or still on a valid visa, or had a visa petition or labor certification filed for him or her several years ago when a law called "245(i)" was still in force.
If, however, the immigrant entered the United States by unlawful means, such as having been a stowaway or crossing over the border through a fence, adjustment of status is not an option. The only possibility is to apply for the green card through "consular processing," meaning the immigrant will attend an interview at a U.S. embassy or consulate in his or her home country. That, however, carries a risk of not being allowed back into the U.S. for many years -- three years if the period of unlawful presence was 180 days or more, and ten years if the period of unlawful stay was one year or more.
If he's been checking in with ICE for 13 years, and was a qualified candidate for deferment under Obama, it's strange that this wasn't presented as an option. That also doesn't explain why ICE was fine with him for 4 years and then suddenly they hit him with a removal order during Obama's Tenure. ---
"History Is Much Like An Endless Waltz. The Three Beats Of War, Peace And Revolution Continue On Forever." - Gundam Wing: Endless Waltz