Obviously the Silents have control of that TARDIS since we saw them operating it in The Impossible Astronaut.
I can think of two possibilities. Either the Silents are be using it to wreck all sorts of havoc, or have they given the TARDIS to River Song as a tool to use against The Doctor. The latter does explain how Mels can insert herself into Amy's past.
I can think of two possibilities. Either the Silents are be using it to wreck all sorts of havoc, or have they given the TARDIS to River Song as a tool to use against The Doctor. The latter does explain how Mels can insert herself into Amy's past.