Why was the Silence ship from "The Lodger" abandoned?

Question

There are a number of things still unanswered from the Silence storyline. Large questions as well as throwaway statements suggesting some connection with a detail from a previous episode that never gets revisited.

I encourage posing additional unresolved plot points, but I'm going to start it out with this:

In Season 6's "Day Of The Moon", The Doctor et al. show up to rescue Flesh Amy from The Silence after she is kidnapped from the orphanage.

When they step out of the Tardis, The Doctor calls our attention to the ship's resemblance to the stranded spaceship posing as a second floor flat in Season 5's "The Lodger":

"Oh. Interesting. I've seen one of these before. Abandoned. I wonder how that happened."

I didn't notice until recently while rewatching what his last sentence suggests. It was the same technology, so it must have been a Silence ship.

How, why & when was the ship abandoned?

Answer 1

The circumstances of the episode imply that it was abandoned in 1969 (or shortly thereafter; emphasis mine):

Doctor: You just raised an army against yourself and now, for a thousand generations, you're going to be ordering them to destroy you every day. How fast can you run? Because today's the day the human race throw you off their planet.

^{Doctor Who Series 6 Episode 2: "Day of the Moon"}

The very strong implication is that the human race quickly killed all of the Silence still on Earth, which would naturally lead to the ship on Craig's roof (which isn't Craig's roof yet, because this is 1969 while "The Lodger" is obviously contemporary-ish to broadcast date) being abandoned.

Steven Moffat all but confirmed it in a 2014 issue of Doctor Who Magazine, clarifying that the ship seen in "The Lodger" was an abandoned ship from the Silence occupation:

David Elham asks: In The Lodger we see a TARDIS-type machine on top of Craig's flat. Then, in The Impossible Astronaut, it appears again, occupied by the Silence. Was it actually a TARDIS or something else? Will we ever find out?

Those were Silence ships. That's how they arrived on Earth, and where they hung out and had parties and games of forget-me-not (is that a game?). So the one the Doctor found in The Lodger was an abandoned ship from the Silence occupation that was in the Earth's past, but - at that point - the Doctor's future. You see it all makes perfect sense if you watch it in the wrong order - he said, accidentally summing up his entire career in the most damning and wretched way.

^{Doctor Who Magazine #475}

Answer 2

I think the answer is that Moffat cleared up all the loose ends that he thought he could (or perhaps should) in The Time of the Doctor, the Christmas special that was Matt Smith's swan song as the 11th Doctor.

A July 2013 interview with io9 contains the following (emphasis mine):

When we caught up with Moffat last weekend at Comic-Con, we asked him, "Do you feel like you owe viewers some closure on the big questions, like who blew up the TARDIS? Or what the Silence was up to?"

And he responded, "Well, we are going to do it all. It's going to end at Christmas. Yeah, [there will be closure]. But 'owe them'? I don't know about 'owing.' But yeah, there's a plan, and we will end the Eleventh Doctor's run with the answers to some of those questions."

Some reviews of The Time of the Doctor include statements to the effect that he did clear up the loose ends. For example:

Kyle Anderson of Nerdist wrote the finale "might leave a percentage of fandom cold, but... I can’t think of a better way for the Eleventh Doctor to end his tenure." He stated, "There were lots of loose ends for writer Steven Moffat to tie up, but somehow he did it."

_{DOCTOR WHO REVIEW: THE TIME OF THE DOCTOR (SPOILERS!)}

While you may still have questions, I suspect that with Moffat leaving Doctor Who, there will be no more answers coming. Unless he decides to drop something in his "Last Christmas" episode: Twice Upon a Time.