Tsukuba is a planned city built around the car, and that shows. The main sights are spread out across a wide area rather than clustered in a walkable center. The central Tsukuba Center mall and Tsukuba Station are fine on foot, but reaching JAXA, Mount Tsukuba, or the University of Tsukuba campus requires a bus or bicycle.
City buses run from Tsukuba Station to most major destinations, including JAXA and the mountain base. A one-day bus pass is available and worth buying if you plan to visit more than one or two sites. Taxis are readily available at the station.
Cycling is a practical option — the city has dedicated bike lanes and the terrain is flat. Rental bikes are available near Tsukuba Station.