Troubled airline United Continental continues to operate under federal investigation by the U.S. attorney's office in New Jersey, while its top official Jeff Smisek stepped down today and the company named Oscar Munoz its new CEO, according to NPR. Munoz comes from railroad operators CSX Corp. where he was the president and chief operating officer.

Smisek, 61, already weathered a lengthy ongoing federal investigation because of claims he may have improperly tried to sway senior officials at the Port Authority of both New York and New Jersey, said the Wall Street Journal.

At the heart of the investigation, former Port Authority Chairman David Samson allegedly used his position to demand favors and personal benefits from United. While Samson was still in office, United and the New Jersey Port Authority were renegotiating contracts under Samson's watchful eye.

One specific point of focus seems to be a reinstated twice weekly flight from Newark, N.J., to Columbia, S.C., which originated when Samson took office and was canceled a few days after Samson left office. The flight left Newark Thursday evenings and had a return flight from Columbia Monday mornings. Samson had a vacation home in Columbia, according to Fox News.

Smisek walks away from United Continental with a $5 million severance package that includes a cash lump sum of $4.875 million, lifetime flight and parking privileges, share awards and the title to his company vehicle, all of which are contingent upon him not being charged with any felony or become indicted for any wrongdoings.

Smisek has been with the company since 1995, when he came aboard as legal counsel, and rose in the ranks to the top slot before his resignation today.