Spoiler:
They weren't lining it out during the story, but the impression I got out of the flashbacks and games were that Cloud and Vincent were both placed into project tanks at the mansion. It was kind of like a healing tank along with fusion with Jenova cells. Cloud ended up becoming something as a ~Sephi-Roth!~ clone and was noted as a "failed experiment." Vincent ended up becoming the FFVII Terra while having the Proto Materia in his chest. Tifa just healed up and went to Seventh Heaven, unless I forgot or missed a story line plot.