Over the next few years as support for the Lebanese Forces declined, and in 1984,
Samir Geagea, Karim Pakradouni, and Elie Hobeika forced the resignation of the then commander of the Lebanese Forces,
Fouad Abu Nadir. Fouad Abu Nadir was considered too close to
Amine Gemayel (he was Gemayel's nephew). Amine, unlike his brother Bachir was disliked by all the LF leaders. Elie Hobeika was named head of the LF after Abou Nader's removal.
On January 15, 1986,
Oliver North led a coup, from the American Embassy in Beirut that removed Elie Hobeika from Lebanese Forces command, mainly due to Hobeika signing the Tripartite Accord with
Nabih Berri and
Walid Jumblatt in full coordination with all forces in Lebanon, active politically, including the Maronite Patriarch. Hobeika was besieged in his Qarantina headquarters by Geagea's men (Elias el Murr was trapped with Hobeika in the same building) and was evacuated by
Michel Aoun after strong American pressures. He and his supporters fled to
Paris. They returned to Lebanon as a pro-Laic LF faction and were stationed in
Zahle. In 1990 Hobeika supported the parliamentary faction against Syria in the war initiated by Michel Aoun.
After the civil war ended in 1990 Hobeika became Minister for the Displaced. In October 1992 he was appointed Minister for Social Affairs and the Handicapped. He was reassigned to the Ministry of Electricity and Water in 1996, a period which saw massive power projects in Baddawi and Zahrani, Zouk And Baalbeck, and massive electrical grid installation and distribution throughout Lebanon, including the outlying areas still in turmoil with Israeli Forces in the south, hence the progress was too slow compared to the massive increase in the Megawatts needed, since little electricity projects were accomplished over 18 years of civil unrest, mainly because of the Israeli operation Grapes of Wrath. In 1998, General Emile Lahoud became president of Lebanon and appointed Selim Hoss Prime Minister.In 2000 Hobeika lost his parliament seat, due to Syrian active interference in the Polls against Hobeika . In June 2001, Chebli Mallat, a left-wing Maronite lawyer, filed a case against Ariel Sharon in Belgium under a law that permitted to sue foreigners for crimes against humanity.Just before his death, Elie Hobeika publicly declared his intention to testify against Ariel Sharon about his involvement in the Sabra and Shatila massacre in a Belgian court's trial for crimes against humanity. A Belgian senator, Josy Dubie, was quoted as saying that Hobeika had told him several days before his death that he had "revelations" to disclose about the massacres and felt "threatened". When Dubie had asked him why he did not reveal all the facts he knew immediately, Hobeika is reported to have said: "I am saving them for the trial". Lebanese Interior Minister Elias Murr has accused Israel of being behind the act, citing a trace on the license plates of the sedan. The case was later dropped as the Belgian law was amended.