This paper summarizes highlights of research results from the Alcator C-Mod tokamak covering the period 2006–2008. Active flow drive, using mode converted ion cyclotron waves, has been observed for the first time in a tokamak plasma, using a mix of D and 3He ion species; toroidal and poloidal flows are driven near the location of the mode conversion layer. ICRF induced edge sheaths are implicated in both the erosion of thin boron coatings and the generation of metallic impurities. Lower hybrid range of frequencies (LHRF) microwaves have been used for efficient current drive, current profile modification and toroidal flow drive. In addition, LHRF has been used to modify the H-mode pedestal, increasing temperature, decreasing density and lowering the pedestal collisionality. Studies of hydrogen isotope retention in solid metallic plasma facing components reveal significantly higher retention than expected from ex situ laboratory studies; a model to explain the results, based on plasma/neutral induced lattice damage, has been developed and tested. During gas-puff mitigation of disruptions, induced MHD instabilities cause the magnetic field to become stochastic, resulting in reduction of halo currents, spreading of plasma power loading and loss of runaway electrons before they cause damage. Detailed pedestal rotation profile measurements have been used to infer Er profiles, and correlation with global H-mode confinement. An improved L-mode regime, obtained at q95 ⩽ 3 with ion drift away from the active X-point, shows very good energy confinement with a strong temperature pedestal, a weak density pedestal, and no evidence of particle or impurity accumulation, without the need for ELMs or any additional edge density regulation mechanism.