Brian is a member of the Others. It is implied he was one of the temporary occupants of Ms. Klugh's decoy village.
After the Others fled from the village, Brian (and possibly several other members of the Others) stayed behind. He inspected whether one of the survivors of Flight 815 would go after their missing friends, who embarked on a search and rescue mission to find Walt Lloyd, led by his father, Michael.
Sayid is secretly being observed at the decoy village. ("Live Together, Die Alone, Part 2")
As his leader Benjamin Linus states, it was intended for them to find it, and for Brian (and the Others) to report back on the incident.
However, after Brian saw one of the passengers Sayid Jarrah as intended, he followed him to the shore.
At the shore, he witnessed Sayid hop on a boat where Jin-Soo Kwon and Sun-Hwa Kwon were boarded on. ("Live Together, Die Alone, Part 2") Then, he informed Colleen Pickett of this.
This occurred during the event orchestrated to take Shephard, Ford, and Austen from Pala Ferry to The Barracks so he was not with Klugh at the time. ("The Glass Ballerina")
It is not made clear how Brian, Colleen and Mikhail Bakunin were unaware of Desmond's Elizabeth sailboat lying unoccupied on the Island for 3 years. It is possible Ben was made aware early on, but hid it. This may explain the expression Juliet gives Ben after he asks Coll how they have a boat.