The first step to rebooting the galaxy the second time is unlocking the Cryopod ship upgrade. You do this by finding the shrine that you desecrated in the start of the game. There is no trick to this, you just have to explore every uninhabited planet until you find the one with the shrine. If you leave your ship and the planet is completely empty (no rocks, no plants, completely empty) then you have likely found the shrine planet! Just find the shrine, take the mundanium away and the shrine's spirit will curse you just like at the start of the game.
Once this is done, the Cryopod will be available to purchase as a ship upgrade for 200,000 credits and 4 upgrade units. (You may or may not need a max cargo lift before the Cryopod becomes available). Once the upgrade has been installed, step into it and reset the galaxy.