One obstacle to the relationship was Charlie's long-time obtuseness with regard to Amita's interests in him, a fact upon which she commented early in season 2. Her interest in Charlie wouldn't be so compounded if only he could not see everything in the world in mathematical categories. On the other hand, she deeply admires his work, and is filled with awe after touching a chalkboard full of his elegant equations. In Season 2, after Charlie became concerned with her association with Dr. Penfield, she stated she had no time for a serious relationship because of her graduate work on astrophysics. She assured Charlie that her interest in Penfield was only of the intellectual nature. At times, she has felt that her work has been subsumed by Charlie's research. Amita's professional career further created a conflict for her following an offer for a three-year assistant professorship at Harvard University. At the close of season two, she had not decided if she would accept the position, or remain in California and apply for a similar position through CalSci. With the start of season three, she decided to take the CalSci position and kindle a romance with Charlie. However, Amita said that it would be arrogant for Charlie to think that she only stayed for him. She is having problems accepting her role as a professor, especially in the view that she was a student only recently at the same university where she now holds a faculty position. Larry Fleinhardt advised her in recreating her image of herself, for only then would other professors accept her as a colleague. Finch said harsh words to Amita about her needing to act like a professor and be more than Charlie's assistant and even stated that she dresses like a kid. Mildred disapproved of her dating her former thesis adviser. This caused her to doubt her relationship with Charlie, but he took it to the next step in kissing her in his garage and she did not hesitate. When Dr. Finch saw this, Charlie and Amita were temporarily shocked. In "End of Watch", she nearly quit chairing the curriculum committee, as their colleagues remarked on their relationship. Amita understood Charlie's sentiments over Larry's leave of absence to the International Space Station and could discern that Eppes had never been in a situation where he was not able to get what he wanted. In "Killer Chat", she stated that she could distinguish between "Professor Eppes" and "Charlie Eppes". Megan Reeves said it was nice that she worked well with Charlie.