How Saul and his sons died
In the battle at mount Gilboa, the Philistines followed hard upon Saul and his sons. They killed three of Saul’s sons: Jonathan, Abinadab, and Melchishua. The archers then struck Saul, leaving him severely wounded.
Saul asked his armourbearer to thrust him through because he feared capture and abuse by the Philistines. When the armourbearer refused, Saul took a sword and fell upon it. The armourbearer then died in the same manner.
Why the question can be confusing
Earlier, Saul pronounced that Jonathan should die because Jonathan unknowingly tasted honey during Saul’s rash oath. The people intervened and rescued Jonathan, declaring that he should not die. Saul therefore threatened or ordered Jonathan’s death on that occasion, but he did not carry it out.
Saul also repeatedly tried to kill David, who was his son-in-law, not his biological son. These separate events can become confused when the accounts are recalled together.
What happened to Jonathan
Jonathan remained loyal to David while still honouring his responsibilities as Saul’s son. He died fighting beside his brothers in the same battle in which Saul received his fatal wound. David later lamented both Saul and Jonathan in 2 Samuel 1.