Hakhmat Othman Hassin Matsarwa allegedly entered Syria to join the Jihad group and find his brother, Hassin, who had left Israel to fight with rebels several months earlier.
Matsarwa, 28, trained in a rebel camp and was later asked to carry out two suicide bomb missions, one targeting President Bashar Assad's regime, and another in Israel.
He refused to carry out the missions, Israeli broadcaster Arutz Sheva reported.
Matsarwa also told officials that the rebels had asked him many questions about Israel and the defense forces, Arutz Sheva said.
Matsarwa was indicted Wednesday for several crimes, including contact with a foreign agent and illegal immigration.
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