There are a couple of ways ... choose the one that suits your operations best.
Let's assume two projects (P1 and P2) and each project has three phases (Initialization, Implementation and Closeout).
1A. Each project creates 3 separate files:
** P1_Init, P1_Impl, P1_Close,
** P2_Init, P2_Impl, P2_Close
1B. Each project creates 1 Master file which links to the three project phase files for that project:
** P1_Master (then click on Insert | Project and insert the three phase files for the project -- remember to keep the box "Link to project" with a click mark).
** P2_Master (repeat as above).
1C. Each Phase also has 1 master file which links to the two project files for that phase:
** Phase1 (then click on Insert | Project and insert the two Phase1 files (P1_Init, P2_Init).
** Phase2 (then click on Insert | Project and insert the two Phase2 files (P1_Impl, P2_Impl).
** Phase3 (then click on Insert | Project and insert the two Phase3 files (P3_Close, P3_Close).
The biggest drawback: Files must always live in the folders once they are created. If you move even one phase file then you'll have to recreate the various Master project files.
2. Use a field (Number1) and enter the phase number for each task and each summary task. You can then autofilter or create a new "Group by" set of criteria to use this field and the Project field.
** P1 contains all phases for Project1 (in other words, you won't have P1_Init, P1_Impl, P1_Close, P2_Init, etc.)
** P2 contains all phases for Project2 (in other words ...)
Drawback: when you want to create a report of all projects for a single phase, you'll still have to create a Master project that inserts P1 and P2.
3. Write some VBA. You have two choices: build a VBA macro in Excel to open each project and pull out the information you want from each Project and pull it into an Excel spreadsheet or write some VBA in each project to push the information from each project into an Excel spreadsheet.
Drawback: how much VBA experience do you have? How well do you understand the underlying object model of Project?