Intakes are the hydrogen ram scoops on the front of the spacecraft which fuel it by gathering the free hydrogen in the space or in the extreme upper atmosphere of gas giants. They refill the fuel tank of the ship.
Intake upgrades alter the effectiveness and the profile of the vehicle; the more effectively a ship takes in fuel the more efficient its engines. The tradeoff is that, unless countermeasures are installed, this also increases the radar signature. The appearance of the ship is altered as well: more primitive intakes look like physical fan blades, others glow different colors as heat capacity increases.