OK, let's start again, but this time let's make it slowly.
Last time we saw Olivia Dunham before this episode, she was on an alternate reality face to face with William Bell. Next scene, now, her SUV is involved in a car crash, but she isn't driving; she isn't there at all. Until the guys show up and Dr. Bishop does who-knows-what, and suddenly Olivia is thrown through the windshield out of nowhere.
(Looks like Walter does have magic fingers - because later in the episode, with gloves and through clothes, he can feel with his left hand how a dead body's anus is soaking wet. Ugh.)
At the hospital, doctors say Olivia's brain damage is irreversible, but looks like she won't take that, as later she wakes up speaking in Greek.
A new enemy is introduced on this episode: a shapeshifter. He is sent there to kill Olivia to prevent a meeting, but whith whom? As he doesn't succeed on the first try, he is sent again to get some information. He fails again, but manages to escape and take a new shape: agent Charlie Francis.
Meanwhile, Broyles is in Washington trying to prevent the Fringe Division of being shut down by a Senate committee.
A New Day in the Old Town seems to settle down what the next several episodes will be all about. A spy, a meeting and a hidden thing Olvivia seems to know about but doesn't remember, a one man fight to keep the Fringe Division alive, and as usal, a lot more questions but not a single answer.
There are a couple nice details on this episode.
One of them is the way the shapeshifter communicates with his people: through a typewriter and a mirror. The authors could have chosen an uber-technified device from another universe, or even a regular cellphone, but they didn't. Instead, they went the old fashioned way.
The other is the double reference to The X-files. Sweet.
Oh, by the way, The Observer was there. :)
(Observer image credit: http://eastereggs.fringetelevision.com/2009/09/fringe-easter-eggs-observer-in-new-day.html)