Brian gets pissed at Games Dean and challenges him to a battle of Field of Fire in rage. While he's on the receiving end of a Curb-Stomp Battle which he is deliberately losing - or at least not trying to win - to get expelled, Jenny enters the game and bails him out, giving him a Rousing Speech in the process.
Before the guild tryouts in episode 9, Brian finds out that Ted and Ki dug his old mouse and keyboard out of the dumpster and repaired them, even though they had been destroyed by the Law. Brian decides to use his old gear for the battle instead of the standard issue VGHS equipment.
In episode 9, Brian tries out for a spot on the VGHS team at last. Once in the game, a couple of players start picking on him. Then:
Games Dean: Hey! I've seen these two cats meow, and it's about to be a fancy feast tonight. (to Brian) You plan on bringing the thunder?
Before the game starts in episode 9, the aloof teacher Ace teases Brian for being late again, but genuinely wishes him luck before Brian sits down.
Episode 3 deals with each character's (except Brian's) parents. Naturally, we already know by this point that Freddie is a Manipulative Bastard towards his son, and Mary Matrix would rather act like a harsh coach than anything like a mother. But then we meet Ki's dad, Ken. After the episode is done, this much is clear; He and his daughter love each other very much. He would like to see her reach her potential, and claims VGHS might not be good enough for her. He does not care who she dates. And they are so close, they play Pokermon with kisses and chores as wagers. It's just the most adorable thing ever.
The end of episode 4. Throughout the episode, Brian has been having difficulty defusing bombs in Field of Fire, even though he claims he can normally handle it just fine. In the match at the end, when Brian is the only one left alive on the team, he has to disarm the bomb. He gets to the bomb and prepares to disarm it, looking nervous...when his pet cat, Cheeto, arrives on a RC car (It Makes Sense in Context), crashes into a wall, flies off the car, and lands on Brian's face. Jenny looks ready to pull Cheeto off...when Brian holds up a finger, silently telling her to hold on. He then manages to successfully disarm the bomb; not despite having a cat blocking his view - because he has a cat blocking his view. He didn't feel right trying to play the game without Cheeto there.
Even better; most viewers who remember the first season will recall that, constantly, Cheeto would attack and scratch Brian. They might think that when Cheeto is on Brian's face, he's just doing what he normally does - being a bother, possibly ready to scratch. Then, for a split second, Cheeto quietly mews and rests his head against Brian's headphones. He is hugging Brian.
Even better when Ki then manages to get Cheeto to become the school's mascot, avoiding having to throw him out as the rules demand, as no pets are allowed.
Episode five seems to be the episode dedicated for jerks with hearts of gold. Calhoun of all people goes out of his way to give some encouraging words to Brian in episode 5 when he hits the Despair Event Horizon, and Law for quite possibly the first time in his life comes to genuinely care about someone after Shot Bot performs a Heroic Sacrifice to help clear the Law's name.
This is followed by Jenny, Ki, and Ted coming to help Brian clean up the mess Calhoun is making him clean.
Calhoun's reaction is especially heartwarming because of all the crap he's put Brian through from the beginning and constantly muttering how he hates him. His first response wasn't anger but understanding that Brian has had a lot of responsibilities put on him that anyone would have trouble keeping up with and just simply couldn't rise to the occasion this time.
When Ki's having a debate against Shane for student president, she declares that she will use the funds to help get better computers for the social gamers that she met earlier, who run on very primitive equipment (to the crowd's chagrin). Later in the episode, the social gamers give Ki their thanks by becoming her new campaign team.
This was also after Ki had accidentally insulted them by saying that they weren't playing "real games".
Jenny referring to Brian as "the only person that's ever truly loved [her]".
The heartfelt moment that Jenny and Mary share in episode 5.
Especially powerful since it's practically the first time Mary has ever actually done any form of true parenting to her daughter.
In the same episode, Brian talks about how before VGHS, he had to take care of himself, since he never really had a dad and his mom was an addict. As a result, he got used to being alone, but after going to VGHS and meeting Ted, Ki, and Jenny, he didn't feel lonely for the first time in his whole life. When he heard that Jenny would be leaving to join her dream FPS team in France, he acted impulsively out of fear of losing her, which he does regret.
Brian: I'm so sorry that I hurt you, Jenny.
After Ki had spent the whole episode acting moody and nihilistic after losing the election, much to Wendell's chagrin, she hosts a 24-hour game jam where she makes a very simplistic game where you walk until you collapse and die. However, she eventually finds herself and expands the game. When Wendell plays it, his expression of joy is just too adorable. You could see the happiness in Ki's eyes. Hell, she was starting to tear up.
At the end of episode 6, the students are celebrating that the school is saved. Calhoun then gives Brian a broom, telling him that there's going to a big mess that needs to be cleaned up, giving you the impression Calhoun is going to palm off all the work to him as always. However, as the camera pans out, it shows Calhoun holding a broom as well, and he cleans up the school alongside Brian.
At the end of the FPS team training (to go up against Napalm), Jenny gives a little speech about how she knows the team will probably lose and that the school will be gone by the next day, but that she doesn't want to leave the school and is at least grateful to spend her last day playing with the team.