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Apophis used his Ha'tak as his command vessel when he and his son Klorel took two Ha'taks to destroy Earth. His vessel's shield was able to withstand a Naquadah enhanced Nuclear warhead launched from Earth. But his vessel was destroyed when SG-1 infiltrated his son Klorel's Ha'tak and planted C-4 all over the ship. After being captured and escaping with the help of Bra'tac they headed to the Pel'tak. When there they took Klorel hostage and changed the course of Klorel's vessel so it was closer to Apophis's vessel. They then disabled the shields on Apophis's vessel and escaped in two Death Gliders. Except for Dr. Daniel Jackson who escaped using the Stargate on Klorels ship. The aftershock of Klorel's vessel exploding destroyed Apophis' vessel. (SG1: "Within the Serpent's Grasp", "The Serpent's Lair")
Since most of Apophis' Jaffa were on board this vessel when it was destroyed he lost most of his Jaffa. When he returned to Chulak, he had only a hand full of Jaffa left who would put their life on the line for him. The others believed that he was a false god and refused to go to join his army. In this time he was vulnerable and didn't have the Jaffa to defend himself if he was attacked. This led to him being captured by Sokar. (SG1: "Family", "Serpent's Song")