I believe, although some claim the ultimania guide states otherwise, that Jenova was controlling Sephiroth, but not in an obvious sense. Essentially she was the force of chaos, or darkness, that, from the background, compels the story's antagonists in different directions, but all towards the same ends, which would result in the destruction of Gaia, or most life on it.

Sephiroth's plan was to move his "clones" (keep in mind this is not the conventional, Western definition of clones) like chess pieces in order to fulfill his goal. From his state of uconsciousness in the Northern Crater, he was able to use "#1" and Cloud (both arriving at midgar at about the same time) primarily to combat Shinra, find the black materia, and deliver it to sephiroth for summoning. Thus, a meteor would threaten Gaia, and the Planets lifestream, and all its energy + knowledge would gather at which point Sephiroth would be the center.

It should be noted that this plan is exactly what happens, even after sephiroth
is defeated, although it takes place at Midgar, not the northern crater.

At this point, sephiroth would basically become one with the planet, at which time this being would be a conscious planetary entity, and we can assume the same 1,000 year storyline would recommence, as it searches for a new planet's lifeforce to consume.

These are obviously Jenova's intentions, and as an actual fetus merged w/ Jenova cells, Sephiroth is, for all purposes, IS Jenova, her will, her child. This is parallel to FFIV's story of zemus controlling Golbez + Kain, or of the sorceress's intentions passing on in VIII