“My Three Crichtons” is episode ten of season two of Farscape.
Pilot and Moya detect an oncoming … thing, that does not appear to even be a physical object, but instead something made of energy.
It enters Moya and examines the crew, before picking Crichton. It also sounds like R2D2.
It envelopes Crichton in a ball of something, before spitting him out. Or, rather, three of him. One is the original, one a rather more primitive version and the final one is a more evolved version. They aren’t simply clones, either, as they have his memories, and believe they are John Crichton.
The sphere is trying to suck Moya through a dimensional portal. Unless one of the Crichtons is placed back inside the sphere.