Bringing the Pieces Together

Above is a time-based cladogram (Chiappe 2009) covering maniraptors. It shows accurately the actual fossil evidence but unfortunately interprets it in a dino-to-bird phylogeny.
You notice the oviraptors and the alvarezsaurids are correctly shown as living well after the origin of the flying dromaeosaurids and troodontids. (Oviraptors and the alvarezsaurids were actually secondarily flightless).

Below is an outline of the development of modern birds from pterosaurs, which is in line with the actual fossil evidence.
In order to follow this, visualize pterosaur lines preceeding and connecting to the dromaeosaurid, troodontid and enantiornithes lines and visualize placing modern birds to the right end of the dromaeosaurids, troodontids and enantiornithes lines. (For flightless birds see details below).
Consider the following concurrent paths:
One path:

By the early Cretaceous, some pterosaurs (by the process of cladogenesis), had developed into flying dromaeosaurids and troodontids (eg. Deinonychus, microraptor etc).
And by the late Cretaceous, many of these flying dromaeosaurids and troodontids had developed into a variety of modern flying birds (Neognaths).

Concurrently, during the Cretaceous, some of the flying dromaeosaurids and troodontids settled on the land, developing by the process of cladogenesis, into primitive flightless birds such as the oviraptorids, the alvarezsaurids, flightless troodontids (eg. troodons etc) and the flightless Ornithomimosauria.
And by the late Cretaceous, these primitive flightless birds had developed into modern flightless birds (paleognaths) such as the ostrich and emu and cassowary.

Another path:
By the early Cretaceous, some other pterosaurs (by the process of cladogenesis), had developed into flying enantiornithes.
And by the late Cretaceous, many of these flying enantiornithes had developed into a variety of modern flying birds (Neognaths).
Concurrently, during the Cretaceous, some of the flying enantiornithes settled on the land/water, and developed (by the process of cladogenesis), into primitive aquatic birds, such as the hesperornithes.
And by the Paleocene, these primitive aquatic birds had developed into a variety of modern aquatic birds, such as loons, grebes and penguins.
I will analyze these steps in the next few posts.

Note that this explanation fits exceptionally well with the fossil record.(It also fits exceptionally well with the morphological evidence as this site has shown in detail).