First, thank you for your service to our country.
Generally speaking, an alien who entered the United States unlawfully is not eligible for adjustment of status in the United States. This is because the law requires an alien to have been inspected by an immigration office and either admitted or paroled into the U.S. to be eligible.
However, since you are on active duty, it appears that your wife may be eligible for what is known as "parole in place" (PIP) wherein she his paroled "nunc pro tunc" (i.e retroactively) to her entry into the United States. This would allow her to then apply for adjustment of status in the U.S. and obtain her residence without leaving the country. PIP does not, however, waive any other grounds of inadmissibility should they exist.
Consult with an experienced immigration attorney who can review you and your wife's situation, determine her eligibility and recommend the best way to proceed. Many attorneys will conduct consultations via telephone or Skype for clients outside their local area.
While this answer is provided by a Florida Bar Certified Expert in Immigration and Nationality Law, it is for general information purposes only and an attorney/client relationship is neither intended nor created. You should seek out qualified counsel to review your case and provide you with advice specific to your situation. Call +1-561-478-5353 to schedule a consultation with Mr. Devore.
Petition for her. She will need to apply for a waiver for her unlawful presence and depending how she entered she may be able to adjust her status to that of a permanent resident here in the US or she entered without documentation she will have to travel to ciudad Juarez to apply. I am no aware of any possible exemptions or special treatment that may exist because she is the spouse of someone serving in the military but there may be. I know that if you are facing deployment you can request for the petition to be expedited. You should hire an attorney to handle your case. One that is experienced in handling family based petitions.
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She seems to be eligible for a stateside waiver. Your military service would be a good background for the waiver. Find an immigration attorney you would feel confortable dealing with and seek the waiver. Some attorneys offer free or reduced fee services of military servicemen in active duty. Immigration is Federal law so immigration lawyers from all over the country can represent you.
NYC EXPERIENCED IMMIGRATION ATTORNEYS www.myattorneyusa.com; email: email@example.com; Phone: (866) 456-8654; Fax: 212-964-0440; Cell: 212-202-0325. The information contained in this answer is provided for informational purposes only, and should not be construed as legal advice on any subject matter.