This high operational activity and its demanding toll resulted in the Southern Command's Alufs (SCA) being replaced fairly rapidly.

After the Egypt–Israel peace treaty, the southern front remained quiet and most of the activity centred on guarding the borders from smugglers and fluid security over the Gaza Strip.

The Gaza Strip, one of the most densely populated places in the world, was known as a stronghold for extremist groups such as Hamas and Islamic Jihad, who engaged in Palestinian political violence.

From 2004, the fighting in Gaza became especially intensive, and on the IDF's part, included targeted killings, short armored expeditions, and efforts to locate and destroy the smuggling tunnels used by Palestinian militant groups to obtain weapons.

As of 2006[update], the attempt to infiltrate Israel to perform suicide bombings and the launch of Qassam rockets, especially by Islamic Jihad and the Popular Resistance Committees, remains ongoing and is the central focus of the Southern Command.