There's a 'secret ending', of sorts. Once you're back in control of Connor, do his epilogue missions. The first one's in New York, the second one is in the frontier, at his village. Then, go to Boston and you'll hear some present-day dialogue instructing you to find Pivots. The game explains how to find them all.
Once you've found them all, you'll get some more present-day dialogue wrapping things up.
If you just want to know what happens, check the spoiler below: After Desmond dies, Abstergo agents retrieve his body from the Grand Temple. They somehow synch his genetic memories to the Cloud, so now Abstergo has complete access to Desmond's genetic profile and can explore his ancestors' memories without him.
There's some foreshadowing for this if you talk to William after rescuing him from Abstergo. He mentions that Abstergo have developed ways of extracting genetic memory from a subject so that anyone can access them, and that they'd probably extracted his and were analysing it to find out where the Grand Temple was.
''Snake from Metal Gear 2 owns everybody. Because he used an owl. To make a guard think it was night time. In the middle of the day. That's just hardcore''