You're not wrong. Over the next few years, Gaster grows increasingly distant and short-tempered with both you and Papyrus. You're not sure what he's doing with his soul research, but your sense of dread grows by the day. Family meals, once full of laughter and good food, are now becoming silent as Papyrus, in his innocent, thoughtful way, keeps trying to draw your father out of his morose depression, but is frequently shut down. Your puns occasionally draw a genuine smile from him, and the metaphorical rain cloud over his head seems to lift for a short time, but even that is starting to not work anymore.
You try asking your friend Alphys and the other lab assistants for answers, but they either make excuses or avoid you, sometimes even going so far as to take another path when they see you coming. Alphys in particular looks distinctly guilty, her eyes nervously shifting from side to side and her stuttering even worse than usual. But she won't tell you what's going on, saying she was given very strict orders not to tell you anything. You're pretty sure that whatever is going on at the lab is having a terrible effect on your father and it needs to stop immediately, but you can't confirm your suspicions without help.
As Gaster's mental state declines, once in awhile you start to catch him staring at you in an unfriendly way. You know it would sound ridiculous if you told someone else, but you have the strangest feeling it's not him anymore. It's someone else. Whenever it happens he quickly looks away, and refuses all further attempts at conversation for hours afterward.
What hurts worse, though, is what he says when you ask him about it later when he seems to be back to normal.
"What in the underground do you mean, Sans? I'm fine! I do not have anything even remotely resembling an identity crisis!" he says, trying to brush you off and pretend like it was nothing.
"then why'd you look at me like that?" you ask earnestly.
"I haven't the slightest idea what sort of look you're referring to! If I looked at you wrong, I apologize. Thank you for your concern, Sans, I know I've been depressed lately, but I'm fine. Better than fine! In fact! I have just made a major breakthrough!"
"that so?" you ask drily, your voice edged with sarcasm. "so everything's just going great. nothin' to be worried about at all."
"Yes! Soon you'll see, when we're all free and you're seeing the sun for the first time! Then you won't have time to worry about trivial, inconsequential things like me accidentally, coincidentally, looking your way!"
You know it was more than that. It feels like a betrayal when he tries to invalidate your perceptions like this. He never did that before making you leave the room with the souls. He always praised and appreciated your ability to see what's going on with people. He often took your advice on how to help others feel better, when they were down.
Your perceptiveness seems to have become an inconvenience for him now, though. You're sure he knows exactly what you're talking about. There's guilt in his expression. There's also confusion and concern in his eye lights as though he wasn't there to observe himself doing what you said, even though he was. That confusion raises your level of concern even more, because you think it might mean he's starting to lose control of his own mind, somehow, though you don't know how.
There's a big party to celebrate Gaster's recent breakthrough, and he and Alphys are commended and given awards by the king for their success. As you watch your father moving through the crowd of monsters, gaily chatting away, you can see the traces of confusion left in his expression. It's far too subtle for most people to be able to pick up. It looks like he's still thinking about your conversation with him. Someone asks you why you look so serious as you hold a cup of punch and try to keep up with the banter among a group of friends. You put on a fake smile and try to act happy, but none of this feels right.
You try to speed up your research for moving through space and time, desperate to give your father another option for getting through the barrier, besides whatever he's doing that's affecting him so badly. The main lab has become an unwelcoming place, so you've moved everything you and your father worked on concerning that research to the workshop that's attached to your family's house. These days, that's where you spend most of your time. With Gaster being so distant, it also helps that you're home all day, so that you can look after Papyrus. Sometimes the two of you mix spatial research with daring escapades and capers.
It's the sort of thing you and Papyrus used to do with Gaster, but he's not interested in "fun" anymore. Papyrus has a very creative sort of intelligence, which makes him incredibly fun to be around, in your opinion. You adore that about him, but Gaster does not. At least, not in his current state of mind where he's forgotten what a sense of humor is. Gaster now only tends to value logical, analytical thinking.
One morning, Gaster stomps over and stares at a puzzle Papyrus is working on, involving how to get all the monsters across a waterway to be rescued, before the rain floods the small island where they are. There is a yellow bird who can carry them across. The yellow bird's left wing is bandaged, implying he might be injured. Only one monster can be carried by the yellow bird at a time, and the bird can only take so many trips before he becomes exhausted, and there's fewer trips than monsters, so at first glance it seems impossible.
Gaster stares at the puzzle for several long minutes, his brow bones furrowing as he is unable to find the answer.
"What is the point of this? There is no logical solution!"
Papyrus is about to answer, but hesitates as he remembers other times Gaster snapped at him. Papyrus looks at you for reassurance for a moment, before gathering his courage to explain.
"Well, you see, that initial discouragement that people perhaps may feel is part of my idea!" he says, quickly forgetting his nervousness in his excitement. "Even though on first perusal of this puzzle, it appears there is absolutely, completely, no way out of this predicament, there is! There is always a way to solve any conundrum or difficulty! That is what I am trying to say with my puzzle!"
The solution, as Papyrus explains it, actually involves the monsters forming a raft bridge over the water and letting the yellow bird walk across the top of them. Gaster doesn't like that, and his ego is damaged by not being able to figure it out. Gaster expresses his annoyance and explains to Papyrus his views on how to properly design a logic puzzle, in his opinion.
You appreciate Papyrus's solution though, because it means the yellow bird doesn't have to be stressed out by carrying anyone, or flying with an injured wing.
When Gaster puts Papyrus down for his unique way of thinking like this, you notice that for several days afterward, Papyrus acts as though he's not as smart as he really is. His puzzles become more obvious and banal. He tries to follow Gaster's instructions, but fails miserably. Straightforward logic is just not how he likes to think. You wonder if maybe Papyrus is acting this way to try to prevent Gaster from attacking him and criticizing him again.
A small fire of anger starts to grow inside your soul as you watch Gaster's behavior towards the two of you worsen. You try to hide it as much as you can to avoid family fights, but you wonder how long you should hide how you really feel.