Presumably, that'd be the work of the Reaper tech TIM had implanted into himself. Those scars certainly aren't there for effect. Terminator-HIX (talk)
It's also assumed to be a form closer to Leviathan enthrallment (temporary) than Reaper indoctrination (permanent). - MA4585159 (talk)
He wasn't indoctrinating Shepard and Anderson, he was rather controlling their movements without their free will (both were obviously struggling physically against an unseen force) LeoJo (talk)
While they weren't immediately indoctrinated, the scene nevertheless is heavily drenched in indoctrination symbolics: the black smoky tendrils around the screen and the screeching noises. Mitranim
Of course the scene shows the Reapers trying to indoctrinate or at least influence Shepard throught TIM, but the actual actions that Shepard is forced to do (specifically, shooting Anderson) happen because TIM is controling Shepards motions, not because his/her indoctrinated mind told Shepard to shoot his mentor, TIM was literally pulling the trigger for Shepard. We can also infer that Shepard executed this action conciously, as we see him/her showing open discontempt for what he/she was forced to do, so we are mostly talking about physical control and less psychological control, like it would be the case with Indoctrination. LeoJo (talk)
TIM could just be a powerful biotic but that's highly unlikely.
Recall that Shepard manages to take a shot at the Illusive man in the end. It's not the only occasion when controlling Shepard ultimately failed; the scientist at Project Rho complaining of increasing levels of sedation is another. Wilson (but not Miranda) made a similar dosage error; Shepard woke from that too. Whatever Cerberus did to him in the way of implants must have been hot stuff.