I think the thing about Janus being a gatekeeper for me is the way it almost seems to stabilize the mental models I have for how he would act in any given situation. Like, I know in my bones that if push came to shove he would be there to help and protect any side. Yes, that's because they're a part of Thomas and he needs to take care of Thomas above all else, but I do think he genuinely cares about all of the sides.
This is a difficult thing to reckon with, given how some of the sides seem to view him. I certainly don't think Roman has ever properly experienced that sort of care.
Virgil, on the other hand, almost certainly has. And yet, there is a sea of bitterness between them.
How does this make sense, then? Well, it's relatively simple. He's a gatekeeper, who only recently stopped being so controlling with hiding things.
Gatekeepers are there so that the host does not realize they are a system. I don't know how to reckon this with how Thomas has been shown to interact with Roman, Patton, and Logan in the past, but I am confident that he was at least responsible for hiding Virgil and Remus from Thomas.
Virgil was not a known variable in early-20s, but obviously was known already at the time of his introduction. I would say that at least by the start of Sanders Sides Janus had begun to cool it on the 'constantly hiding things from the host', but obviously not fully.
Hiding an alter is an incredibly controlling thing to do. It's also something that is done for the Host's benefit, at least in theory.
Being a hidden alter often results in bitterness and resentment. There will often be some conflict between them and the gatekeeper just because of that.
And yet, it is also Janus's job as Self-Preservation to take care of all sides. This fits with him being a gatekeeper; as stated before, the desire to hide things is coming from a place of care. That doesn't necessarily mean that all gatekeepers are also caretakers, but Janus certainly is.
So. Virgil knows Janus. He knows him better than some sides but still not nearly as well as he should given how long they've known each other. Janus knows Virgil, and he knows him better, because Janus is observant. More than that, even-- he needs to know as much as he can to be able to plan correctly, to be able to know what is needed and be ready to nudge things along quietly. He will keep any secret, but he will know all of yours, whether you tell him them or not. You will know as little of his as possible. This is pure selfishness and entirely necessary in his mind.
Janus is caring. He is caring, in an unfaltering manner, that is still not enough. He will help take care of you. He will hurt you trying to do this. He will unflinchingly tend to your every wound and take care of you when ill and he will encourage you to take care of yourself and he will mean it. He will not be emotionally vulnerable. He will not give you anything that you could use to hurt him, which means he cannot show weakness. He cannot show his wanting, his desperation, the true extent of his feelings, because the moment you know someone cares about something, the easier it is to hurt them. He knows this well because he knows how to hurt every side in an instant; he knows their vulnerabilities, they're not hard to spot.
But he does care. And as much as he tries to hide it, you can see that he does. He wants what is good for Thomas. He will cleave through everything else to get to that. Even if it means hurting parts of Thomas along the way, so longer as it is better in the end, it will have been worth it.
Virgil was hidden. He was hidden because Thomas thought that his anxiety wasn't really a helpful voice to listen to, and because it only started getting stronger later. Janus hid Virgil because it would be best for Thomas. Virgil learned, at some point, that he was not welcome.
This was true. He was not welcome. But when we see Virgil for the first time, Thomas is clearly already aware of him. Janus is no longer making an attempt to hide him, and therefore we can interpret all of his behavior up to part one of AA as tacitly approved by Janus; not significant enough to be worth trying to fully silence.
But Virgil ducking out had to be something Janus would have disliked. It impacted Thomas poorly! He is acting unwell! That's something Virgil did of his own accord.
In part 2 of AA we gain insight that the idea of Virgil being unwelcome is 1- something he has held as an internalized belief for some time 2- something he decided to 'fix' by no longer showing himself to Thomas. If there was period where Virgil existed, but Thomas was unaware of him, this is, in his mind, just going back to that. Except it isn't, because his influence still worked even though Thomas was not consciously aware of him. Certain desires or thoughts were expressed via other sides rather than him directly. (see- how Vision acted after the date. He is attempting to verbalize the fear that Virgil was responsible for, because it needs to be talked about and Virgil isn't a part of this discussion.) He existed as something more subconscious; something Thomas could feel, but may not have the insight or vocabulary to properly express.
By the end of AA Virgil discovers he is welcome. And what else can that be but a shattering of his worldview? How else can you feel toward the one that hid you and told you that you needed to stay that way except bitter? Even if Janus has begun to improve things, by this point he is still keeping himself and Remus hidden. There are definitely still issues there. Janus will help Virgil, but he will help Thomas first. And for Anxiety, that can be scary. Thomas spent the first half of the series 'combatting' Anxiety. Even if he wants to work with Virgil now, who's to say Janus agrees with Thomas on that?
So he leaves. What else can you do but leave?
And Janus, now, has been abandoned by someone he cared for as best he could for years. He loves Virgil. He loves every part of Thomas, he loves Thomas. Thomas doesn't even know he exists right now. Has he even thought about showing himself?
Janus was given authority and power by Thomas's mind. By the way Thomas thinks about what he represents as a concept, he became the way he was. Janus had no say in this. Janus does not have a unique age or authority that makes him especially more qualified for this role. He is a side, as much as any other. His position as gatekeeper is a burden to bear. It forces you to manage and choose between alters. His position as a caretaker is a burden. He must be ready for the worst case scenario. He is a break-in-case-of-emergency box, the reserve. It does not come often, but he must be ready for it, and he must do maintenance at all times to stead off what he can. He must do all this without being seen by Thomas, without being known or trusted.
His friend has left him behind, and he can only think that it was a fair choice. It was the best choice for Virgil himself; it was perhaps the most personally selfish thing Virgil has ever done. On some level, Janus has to respect that. On some level, Janus knows he did not give enough to Virgil; he did not do his part to build trust between them. He didn't go out of his way to do something for him unless he was asked. He didn't hug him enough.
And now they are apart and have hurt each other time and time again. The gap between them is bigger than perhaps it ever has been. The anger is growing cold, and that is a danger sign, because it is an apathy towards each other sinking in. They needed space, and they got it, but now to get back together, someone needs to take the first step. And Virgil and Janus are so fucking stubborn. So they stand across from each other, and do not move an inch.