Previously, Miles and Phin hid a trophy together, the trophy is located on a church which is in the southern area of the Financial District. Once here the trophy is on the other side of the tall spire (the side facing away from the road). It is a small square box and after interacting with it there will be some short dialogue and you will unlock the trophy.

The science trophy is the same cube that Miles placed on top of the church in the center of the Financial District at the end of the previous game.To get the trophy, first choose Miles and climb up the church to reach the bell, you will see a blue cube on the side facing the church yard. Go next to it and press  so that Miles will talk to Phin. After he finishes his talking, you will get the trophy.

Where to Find the Science Trophy