It broke her. He said the he didn't trust her. Watching him fight against the guards holding him yelling at her, he was pissed that she stopped him from getting the revenge he sought for 10 years.
She loved him. Nikita loved Michael more than she loved Daniel. She loved Daniel she did. He almost filled the void she felt that ached for Michael. She knew he loved her but she also knew that he would never break proto-call.
She promised him years ago that when the time came she would help him avenge his family's death. She never meant this though; she never meant at the expense of him life.
She spent years making plans to take down Division, but they were each other's Achilles' heel. It made it harder for her to take them down with him being on her enemy's side.
The one thing they always had was trust. It was what kept them going. It was a routine. Division caught up to them and Michael could never take her down. They couldn't kill each other.
Then when they were finally reconnecting by finding Kasim, but he had to make it into a suicide mission. He said he didn't trust her. Her heart shattered. She didn't have the will to fight anymore. She needed to end Division quickly and efficiently. She was tired of all this.
Nikita and Michael parted. Nikita went home and eventually made contact with Alex. She told Alex it was time to get a move on. They needed to destroy the boxes and blow Division up. She had Owen and Ryan to help so she hoped that they could get this done within a few months.
She knew that she would see Michael again, but it was needed. She wanted to stop all together, but she needed to do this for Alex. Even though she was tough and most would think it was a great mentor/student relationship; she had come to think of Alex almost as a daughter.
Alex needed this. Owen needed this. And she needed this for Daniel, herself, and Michael. She still wanted to help him so if she ever got the chance she would kill Kasim in a heartbeat.