After the Crimson Squad and everything attached to it, Gippal went into hiding until the defeat of Sin. The only place we know he hid was somewhere in the desert with a group of other Al Bhed. Sometime while out here, Sir Auron came upon their camp and gave an inspiring 'pep talk' so to speak to Gippal (which is featured on Gippal's Sphere). Unfortunately, his newly planned battle against Yevon is interrupted by the Guado attacking Home. We see Gippal run off with the other Al Bhed to help defend the compound, but we don't actually know if he reached his destination. If he did, it's plausible to assume that he made it onto the airship with Yuna and her guardians.
Post-Sin, we are led to understand that Gippal created the Machine Faction. We don't know at precisely what time or for what exact reason (though there are several theories), but he obviously cared a great deal about Spira's progress and betterment. We do know that there was enough time in-between Sin's defeat and the Machine Faction for Djose Temple to fall into disrepair, and that when Gippal came along he and the other Faction members got it into working order. Djose was undoubtedly chosen for several reasons: it has an obvious relationship to Ixion, Aeon of Thunder, there's a nifty set-up for registration in a separate building versus the main headquarters, plenty of internal room to spread out and work on parts, and most importantly, it had floating rocks and built in lightning decorations. Who wants to bet that Gippal set up business at Djose for the floating rocks alone?