From neobyrth:
This is a spoiler-free walkthrough. To the best of my ability, I have made sure not to give away any of the story of this game so you can enjoy that on your own. It’s meant to help you through any or all of the sections that you want help with. If I missed something or you have any other questions, let me know.

Main Walkthrough
Chapter 1: What Might Have Been
Chapter 2: A Day In the Life
Chapter 3: Punctuality is the Thief of Time
Chapter 4: All in a Day’s Work
Chapter 5: A Meeting of the Minds
Chapter 6: Cat and Mouse
Chapter 7: Pride and Prejudice
Chapter 8: Sugar and Spice
Chapter 9: When Aliens Attack
Chapter 10: When Good Men Go Bad
Chapter 11: The Underworld of Crime
Chapter 12: Shocking Developments
Chapter 13: Cleaning the Slate
Chapter 14: Burning Bridges
Chapter 15: To Save the City
Chapter 16 & Chapter 17 - Ending

Hint Markers
Manhattan Village, Harlem, Morningside, El Barrio
Central Park
Upper East Side
Lower East Side
Midtown
Tudor City
Roosevelt Island
Gramercy
Flat Iron
Chelsea
Garment District
Theater District
Greenwich Village
West Village
Upper West Side
Lower West Side
Tribeca
Soho
Civic Center
Financial District

Miscellaneous Missions
Arcade
Pedestrian Missions
Upgrades