The 19-year-old, who arrived as an under-23 player from Northampton Town in the summer of 2024, established himself as a key part of Graham Coughlan’s squad during the second half of the season.
Scott was a regular in the matchday squad from the start of March and made his National League debut in a 3-0 midweek win over Yeovil Town.
He made five senior appearances in total, as the Pilgrims successfully avoided relegation from the National League.
Scott will now remain with the Pilgrims until June 2027 following the signing of his new deal.