After 1993 Hamas's military wing carried out suicide bombings in Israel in an attempt to derail both that agreement and further negotiations. Hamas supporters were prominent among those who challenged the Palestinian Authority (which was dominated by Al Fatah, the main faction of the PLO), and its leaders have been subjected to mass arrests. The organization opposed the 1996 elections held in the Gaza Strip and the West Bank for the Palestinian Authority legislative council but did not call for a boycott; some Hamas sympathizers ran as independents. In 2004, Israel killed Sheikh Ahmed Yassin, Hamas's spiritual leader, in retaliation for continued Hamas attacks, and subsequently Hamas military leaders based in Damascus, Syria, became more influential than the political leaders in Gaza.

In 2005 Hamas ran strongly in local elections in Gaza and the West Bank, besting Al Fatah in many areas, and in the Palestinian Authority (PA) legislative elections in Jan., 2006, it won a majority of the seats and then formed a government. Accelerating tensions between Hamas and Al Fatah threatened to dissolve the PA in chaos in the spring of 2006, but when Hamas forces captured (June) an Israeli soldier and held in him in the Gaza Strip it provoked a major Israeli incursion into N and central Gaza and renewed fighting. A political stalemate with PA President Mahmoud Abbas over recognizing Israel and other issues led to tensions with the PLO that erupted at times into fighting in 2006. In 2007 Hamas and Al Fatah agreed to form a national unity government, but continuing clashes led to Hamas's seizure of control in the Gaza Strip (June, 2007), which then led Abbas to install a new government without Hamas. Israel subjected the Hamas-controlled Gaza Strip to a blockade. A new cycle of Hamas-Israeli fighting that began in Nov., 2008, led to another Israeli invasion of the Gaza Strip in Jan., 2009.