Research on the Alcator C-Mod tokamak has emphasized RF heating, self-generated flows, momentum transport, scrape-off layer (SOL) turbulence and transport and the physics of transport barrier transitions, stability and control. The machine operates with P-RF up to 6 MW corresponding to power densities on the antenna of 10 MW m(-2). Analysis of rotation profile evolution, produced in the absence of external drive, allows transport of angular momentum in the plasma core to be computed and compared between various operating regimes. Momentum is clearly seen diffusing and convecting from the plasma edge on time scales similar to the energy confinement time and much faster than neo-classical transport. SOL turbulence and transport have been studied with fast scanning electrostatic probes situated at several poloidal locations and with gas puff imaging. Strong poloidal asymmetries are found in profiles and fluctuations, confirming the essential ballooning character of the turbulence and transport. Plasma topology has a dominant effect on the magnitude and direction of both core rotation and SOL flows. The correlation of self-generated plasma flows and topology has led to a novel explanation for the dependence of the H-mode power threshold on the del B drift direction. Research into internal transport barriers has focused on control of the barrier strength and location. The foot of the barrier could be moved to larger minor radius by lowering q or B-T. The barriers, which are produced in C-Mod by off-axis RF heating, can be weakened by the application of on-axis power. Gyro-kinetic simulations suggest that the control mechanism is due to the temperature dependence of trapped electron modes which are destabilized by the large density gradients. A set of non-axisymmetric coils was installed allowing intrinsic error fields to be measured and compensated. These also enabled the determination of the mode locking threshold and, by comparison with data from other machines, provided the first direct measurement of size scaling for the threshold. The installation of a new inboard limiter resulted in the reduction of halo currents following disruptions. This effect can be understood in terms of the change in plasma contact with the altered geometry during vertical displacement of the plasma column. Unstable Alfven eigenmodes (AE) were observed in low-density, high-power ICRF heated plasmas. The damping rate of stable AEs was investigated with a pair of active MHD antennae.