try using some of the shaders in the transparency chanel and changing them over the time line so that you bet both decreasing transparency and a moving transparency. An ecample would be set transparency to mixer with the blendermarble, celular, waves (try them each for effect) set the two colores as both black (all transparent) then over the time line that you want the ship to decloak start changing just one color from black to white (some will now be less transparent) during the same time modify some of the shader properties to give the effect of the transparent sections moving about the ship as it decloaks. the end point should be both colores white (no transparency). If I remember correctly in Startrek they would decloak in a wavy pattern, try using the wave shader under four elements shaders- you will have to play with it, my first test found that you have to apply the mixer in the color chanel also with you texter in one and black in the other to get full transparency- I will work on it some more tonight if I can and post some infor but have to go to work now.