Hello,
I'm a Cornell MEng student right now. It's mostly for people who are planning to go into the industry and work, but doesn't mean it's stopping you from moving onto a PhD after you get your MEng. You can:
1) Use the work you did here and apply to other PhD programs. This is what I did, and I just got accepted to PhD at Michigan.
2) Enroll in the "research track" of the MEng program. That is, you do 7 credits of thesis research per semester (other MEng students do a total of 8 credits of project for the entire year). If you can find an advisor to fund you during the year, then you may ask your advisor to sponsor you for an internal change of status which switches you over to the PhD program right after you get your degree.