Even though he opened the door, Thankappan was still hesitant to actually get in. Unlike Lonappan, he didn't have a great relationship with Ponnappan. What they shared was a working relationship where Thankappan took Ponnappan's orders, no matter what or how shitty it was. That was the life of the junior agent.
Although the Ponnappan he saw with Lonappan seemed extremely friendly and approachable, he was still the commanding officer of the MIB: Snehatheeram base. So, Thankappan was extremely worried since he just committed treason now that he thought about it. After all, he just helped an alien pursued by the MIB HQ. He was slightly worried about the consequences.
"Aren't you gonna come in?" Ponnappan asked from the inside. Thankappan hadn't even completely opened the door yet, so he was surprised that Ponnappan knew that it was him.
"Ah, yes sir." Thankappan broke out of his trance and got inside Ponnappan's office.
