It’s great that you've improved your GPA and gained research experience. While your earlier grades might not look ideal, many PhD programs take a holistic approach, considering your overall journey, research, and motivation. A strong Master's GPA and research experience will be important factors. Don't give up—reach out to programs to get a sense of how much weight they place on earlier grades.
If your advisor’s interests are in a different department, try these:
Talk to your advisor about connecting with other faculty or exploring interdepartmental research opportunities.
Look for a co-advisor or additional mentorship within the department that aligns with your interests.
Adjust your research focus to incorporate your advisor’s strengths while pursuing your interests.