You want something like this?

The gif is poor quality so doesn't look great and full cloak is only for 1 frame but it gets the idea across.

1. Make sure there is a keyframe with the full regular texture.
2. Move the time scrubber to where you want full cloak.
3. Select all parts of the object with the same texture (easier done if they have been assigned to famalies).
4. Go to material lab and select blend transparency from the drop-down menu and then set transparency to 100.
5. Do this for all material groups of the ship. (warning if you just select the whole ship it will just take on a random material of the ship).

To uncloak follow the same steps except set transparency to 0.