In 2001 MARAD removed the Lincoln from the RRF due to her antiquated cargo handling capabilities and she was placed into inactive reserve status. Listed as being stripped of usable materials in July 2009, the Lincoln was finally sold for scrapping at ESCO Marine in Brownsville, TX and was removed from the Reserve Fleet in April 2011.
Towed to BAE Ship Systems for the customary drydocking, hull inspection and stripping of marine organisms from below the waterline, the Lincoln's hull was found to be in a perilously unsound condition. MARAD officials cancelled her planned tow to Texas due to the risk of her loss while under tow, and negotiations were carried out with ESCO Marine and Mare Island's Allied Defense Recycling, which had just purchased the Lincoln's sistership SS President. Knowing the SS President was in a far more sound state and could survive the tow to Texas, the two companies agreed to swap the identical vessels. Undocked from BAE Systems drydock on May 5th 2011, the Lincoln was hastily towed to Mare Island immediately drydocked and readied for scrapping.