According to the book on the Journal of the corps of discovery they were missing for a couple of years and feared dead. They lost contact going west in South Dakota, They took a bad route to cross the mountains didn't see any ships in Oregon. On the way back snow caused a lot of delays and they spent a lot of time with the Nez Perces. When they got back to the Missouri River and their boats , they made it back to St. Louis in a hurry and the News erupted with their account of survival. A source http://lewisandclarkjournals.unl.edu/read/?_xmlsrc=introduction.general.xml

In addition I would like to ask: when they arrived back in Washington, where did they go? Did they just walk back to the White House and greet Thomas Jefferson? Were there any formality or celebrations for their expedition?