We are developing the Birdy concept of a scientific interplanetary CubeSat, for cruise, or proximity operations around a Small body of the Solar System (asteroid, comet, irregular satellite). The scientific aim is to characterise the body's shape, gravity field, and internal structure through imaging and radio-science techniques. Radio-science is now of common use in planetary science (flybys or orbiters) to derive the mass of the scientific target and possibly higher order terms of its gravity field. Its application to a nano-satellite brings the advantage of enabling low orbits that can get closer to the body's surface, hence increasing the SNR for precise orbit determination (POD), with a fully dedicated instrument. Additionally, it can be applied to two or more satellites, on a leading-trailing trajectory, to improve the gravity field determination. However, the application of this technique to CubeSats in deep space, and inter-satellite link has to be proven. Interplanetary CubeSats need to overcome a few challenges before reaching successfully their deep-space objectives: link to ground-segment, energy supply, protection against radiation, etc. Besides, the Birdy CubeSat --- as our basis concept --- is designed to be accompanying a mothercraft, and relies partly on the main mission for reaching the target, as well as on data-link with the Earth. However, constraints to the mothercraft needs to be reduced, by having the CubeSat as autonomous as possible. In this respect, propulsion and auto-navigation are key aspects, that we are studying in a Birdy-T engineering model. We envisage a 3U size CubeSat with radio link, object-tracker and imaging function, and autonomous ionic propulsion system. We are considering two case studies for autonomous guidance, navigation and control, with autonomous propulsion: in cruise and in proximity, necessitating DeltaV up to 2m/s for a total budget of about 50m/s. In addition to the propulsion, in-flight orbit determination (IFOD) and maintenance are studied, through analysis of images by an object-tracker and astrometry of solar system objects in front of background stars. Before going to deep-space, our project will start with BIRDY-1 orbiting the Earth, to validate the concepts of adopted propulsion, IFOD and orbit maintenance, as well as the radio-science and POD.