When Jason Bourne visits the bank in Zurich, he gets ahold of his safety deposit box and, inside, finds several passports, cash and a Sig Sauer SP2009 pistol. Shortly thereafter, he takes the passports and money and leaves the gun in the box. He also gets ahold of another SP2009 briefly while at the US Consulate in Zurich after agents attempt to take him into custody. Bourne tosses the gun in a trash can while making his escape.
During the filming process, the same SP2009 could've been used in the bank and embassy scenes.