Nikki and Paulo were actually the first survivors to come across the drug smugglers' plane shortly after the crash. They saw the plane on the edge of a cliff, but Paulo refused to go up and search for a radio because he was sure it would fall. They also discovered the Pearl hatch and opened it, but Nikki did not want them to go inside. ("Exposé")
The drug smugglers' plane was later seen on the Island by Locke in a dream, a vivid vision of the plane crashing, his mother, and Boone covered in blood. Locke then took Boone into the jungle, following his foresight. Upon finding the plane and suspecting there could be a radio inside, Boone climbed into the plane at the behest of Locke, whose legs were not functioning properly at that time. Inside the plane, Boone tried to send a distress call using the cockpit radio. As the plane began to tip from Boone's weight, he heard a return transmission from Bernard. The plane then fell to the ground below, fatally injuring Boone.
Paulo later returned to the Pearl and overheard Ben tell Juliet to have Tom move the plane on top of the Pearl hatch.
When Eko and Charlie find the plane in the jungle, Eko takes the cross his brother was wearing, puts a statue in his arms, and ceremonially burns the plane, while he and Charlie recite the 23rd Psalm. Eko then tells Charlie that he is a priest. Charlie took at least one Virgin Mary statue with him when he stopped at the plane with Sayid while looking for Rousseau who had taken Claire's baby Aaron away from her, and would later return to take more and hide them.
Later, we find that the plane when viewed from the cliff appears to be lying next to a large circle on the ground marking the site of the entrance to the Pearl. ("?") Locke returned to the site, along with Sayid, Desmond, Paulo and Nikki to find Eko and visit the Pearl. Eko investigated the plane, and Yemi had gone, despite large boulders remaining unmoved by the doors. ("The Cost of Living")
The circle was first seen in episode "Lockdown" by John Locke. During a lockdown incident, Locke was trapped under one of the Swan station's blast doors. Moments before the doors rose again, a blacklight switched on for a few seconds, revealing a large handdrawn map. A noticeably large "?" was drawn in the middle of this hidden map. Later it was revealed the map was drawn by Radzinsky and Kelvin Inman. Their motivations are still unknown.
In the Access: Granted on the Blu-Ray DVD, the Pearl was confirmed to be the question mark on the blast door map.
Main Article: Locke's map
Locke later tried to recall what he had seen and attempted to draw a small map in episode "S.O.S.". After a few attempts he was able to produce something useful.
Main Article: Locke's dream
Main Article: Eko's dream
When Mr. Eko is in the Swan, his deceased brother (Yemi) tells Eko to help Locke and "make him take you to the question mark". The Countdown Timer and the computer keyboard in the dream do not appear as normal and display only question marks. This dream inspires Mr. Eko to start a search for the question mark. ("?")
Main Article: Locke's Dream
After knocking him out, Mr. Eko is able to let Locke show him his map of the blast door. By telling him of his prophetic dream, he is able to convince Locke to start a search for the question mark. The two stumble upon the drug smugglers' plane and make camp, to "wait for further instructions" according to Eko. Locke then dreams how he is Mr. Eko and climbs the nearby cliff, following Eko's brother Yemi. After reaching the top, he sees Yemi in his wheelchair and falls off the cliff, waking up as he hits the ground. After hearing of Locke's dream, Eko decides to climb the cliff. After reaching the top, Eko looks down. He sees a large circle on the ground. The ground had been salted to in order to form the circle but some of the grass had grown back by this time. ) ("?")
Main Article: The Pearl
After seeing the circle, Eko climbs down and starts inspecting the ground. The ground has been salted to make the mark permanent. "I believe they made a circle -- a target -- so that this place can be seen from up above". Right under the plane he discovers something metallic. Locke and Eko move the plane and find a hatch covered with sand. They open the Hatch and discover yet another DHARMA Initiative station. Their search for the question mark thus led them to The Pearl. ("?")