Marcy discovered she was pregnant with Stuart while dating Stu Beggs. At first, she told Stu the baby was his, but came clean about in ...And Justice for All, revealing that Charlie was the actual father.
Stu was born two and a half years before the beginning of Season 5, and arrived with Charlie at the airport to pick up Hank Moody. Hank sees Stuart as a nephew, already seeing Charlie as his brother. Stu is still incapable of speaking, even at two and a half years old, with Marcy and Stu say is completely normal.
While peeking at Marcy and Stu having sex, Charlie quickly discovers Stuart watching.