We were promised hella deaths on Sunday night's Game of Thrones Season 6 finale, but before that big event, we were treated to a little solo hit job. Maester Pycelle got offed at Maester Qyburn's command, but why did the little birds kill Pycelle on Game of Thrones? It was all a part of the plan.
On his way to Cersei and Loras' trial, Grand Maester Pycelle is stopped by one of Varys' little birds. The child whispers something to him, and he reroutes down to Qyburn's creepy lab. Apparently, he believes that Tommen has been stashed down there for safe keeping and that Cersei sent the child to tell Pycelle to go fetch him. Once Pycelle gets to the chamber, however, he realizes that Tommen isn't there, and something is about to go wrong. He tries to talk his way out, but Qyburn traps him. A whole flock of little birds appear out of the woodwork, all with knives. They descend upon Pycelle and stab him many, many, many times.
As if the death isn't gruesome enough as it is, Qyburn chillingly declares, "Sometimes, before we can usher in the new, the old must be put to rest." While it doesn't quite make sense in the moment, now that the episode is over, we know that "the new" Qyburn is referring to is Cersei's imminent rule. Though, to be fair, not even Cersei knew that Tommen would off himself, leaving her to ascend the throne.
Pycelle and Cersei have had an on-again-off-again relationship, in terms of loyalty, so it's not a huge surprise that she presumably gave the word to kill him. In the books, it's actually Varys who carries out Pycelle's death, but it looks like Cersei and Qyburn might have hijacked the little birds for the television series' purposes, and they're the ones behind his murder. It's possible that Pycelle knew about the wildfire stores, and Cersei didn't trust him not to rat her out once he put together her plan. In any case, Cersei is now inexplicably Queen of Westeros, after Tommen and Margaery's untimely deaths, so she'll need all the trusted minions she can gather. Pycelle just didn't make the cut.