Is grad school out of the question? I am a current chemical engineering student with a 2.8 GPA and two years research experience and one paper in the works of being published. Is being admitted into a chemical engineering or bio-engineering masters program an unattainable goal?
No, but you'll want to choose the institution(s) you apply to rather carefully, take great care with your application, and have some bang-up recommendation letters.

Before sending your applications, perhaps you'd like to take a little time to enroll in some upper level courses in your target field(s) as a non-matriculated student, hopefully with some excellent grades coming out of those.

The fall semester would be a great time to do that.