In the High Energy Lab, you can slide an energy ball to open a window in the wall. Then take 2 warp cores, one black and one white, on the right wall and put them in the slots under the window. This will create a black hole and a white hole in front of you. If you launch your probe in the black hole, it will exit via the white hole.
Next, power the two cores by sliding the energy ball behind you upstairs. Your probes will now exit the white hole before they enter the black hole.
To unlock the achievement, you must launch your probe, and remove the black warp core before the probe enters the black hole but after it has exited via the white hole. This will create two versions of your probe. And voilà, you broke the universe !