Recently, I did broader research (read the manga version). Based on this, I would like to give a try to answer my own question.
Disclaimer: I do understand that manga and anime of Arpegio of Blue Steel is completely different story but some concepts overlap and there is a possibility that manga-based explanation would work for anime too.
In manga, Osakabe Tojurou gave Makie false memories about her past and her family. According to them, Makie had a grandpa, whom was deeply attached emotionally to. Tojurou used the opportunity that I-401 departed from Yokosuka port (2 years before original plot) and tuned the false memories that her grandpa wend aboard and did never return.
The thing is, Makie heard somehow that I-401 arrived back in the port and planned escape from mansion in order to see her grandpa.
Fact that can help confirm the hypothesis:
- She appeared near the same Hangars when found Kirishima's core and Haruna. It was on her way to Yokosuka port.
Fact that can help deny the hypothesis:
- In manga, her stuffed bear named Yotarou was gift given by grandpa. In anime we can see photos that she received it from Tojurou himself.