What a thoroughly fantastic concept! I absolutely love shake-ups in gameplay, especially when it serves the narrative. Shame there's no fantasy bit in between the spy part and the showdown, I would have liked to see how you'd handle that. Great work with the art and the music as well - every element perfectly complements one another.
Now, I think the text sticking to one place is a detriment to the pacing, as I would like to play rather than stick around waiting for the text to scroll. It also sometimes goes off screen, though this only happened a few times during the later sections. Would also say the game can be a bit overly punishing sometimes, especially in the sidescroller bit. Some more lives or at least a smaller hit box would easily make this experience more enjoyable. At the end of the day though, these are mostly nitpicks.
Keep it up! I love the imagination you showcase here, and I hope all of you work on more projects together.