Beginning his acting career in commercials at age five, Morgan moved with his family from his Chicago hometown to Los Angeles in 1997, ready to make a go of a serious acting career. Soon he was lensing "Barney's Great Adventure" and landing guest roles on series such as "Touched By an Angel" (CBS, 1997) and "Baywatch" (syndicated, 1997) as well as making his film acting debut in the little-seen comedy "Family Plan". Beginning in 1998, Morgan essayed the role of Scott Anspaugh, a child cancer patient on "ER". The recurring role saw the young actor handling the emotionally challenging role with great aplomb. Dealing with the rigors of chemotherapy and the harsh realities of mortality, Morgan's character was a brave and understandably angry boy, and the actor succeeded in making the character all too sympathetic, leaving audiences breathless when the boy finally ended his painful bout. Heralded as one of the finest moments in contemporary series television, the scene was moving due in no small part to Morgan's notable skill and palpable warmth.
Morgan next reached a wide audience tormenting Haley Joel Osment's sensitive Cole in the acclaimed thriller "The Sixth Sense" (1999). Television productions like Showtime's "In the Doghouse" (1998) and The Disney Channel's "Genius" (1999) offered the actor some less taxing comedic roles, while back on the big screen he was battling British baddies as a preteen who must wield a gun to help his reluctantly involved former warrior father (Mel Gibson) protect the family in "The Patriot" (2000). Morgan would continue to use his innocent looks and acting experience to his advantage, often playing children in emotionally and physically challenging positions. In the festival-screened "A Rumor of Angels" (2000) he portrayed a grief-stricken boy who turns to an older woman (Vanessa Redgrave) to help deal with the loss of his mother (Catherine McCormack) while "Jurassic Park III" (2001) cast him as an adventurous aspiring paleontologist who has only his wits and wisdom as protection from a world of genetically-engineered dinosaurs when he is marooned on the infamous Isla Sorna. The thriller "The Glass House" (2001) co-starred Morgan and Leelee Sobieski as a pair of heirs to a fortune entrusted to some seemingly shady guardians (Diane Lane and Stellan Skarsgard) following their parents' untimely death. Other projects included "The Rookie" (2002) wherein he played the young incarnation of Dennis Quaid's high school baseball coach tuned MLB expansion team player.