The key to making sense of the Reese/Stevie/Malcolm story lies in the dialogue between Reese and Malcolm prior to the Robo-Stevie break-in. I quoted this in the Voting Community page. I'll repeat the quote of the "meaty" part here:
Reese: "You and Stevie are going to be friends your whole life, but once you go to college and you're not stuck with us, we are never going to see each other again. But even so, you're spending the rest of the time left with Stevie, instead of ..."
[Embarrassed silence--resumes doing pushups]
Malcolm, muttering: "Do I have to tell you I love you?"
Reese: "No."
Malcolm: "Good. Dude, like you said, we're brothers. It doesn't matter if I don't want to be here. I'm stuck here. No matter where I go or what I do, we're always going to be forced together: Christmas, birthdays--we're going to be forced to be around each other for the rest of our lives."
Several on-going themes are tied together in this exchange:
--The male taboo against talking about feelings toward other males--Reese can't bring himself to finishing the sentence "instead of..." This leads to bottled-up resentments that get pent up until they reach the breaking point, as they did in Reese's first scene with Stevie.
--The anxiety Reese feels about coming adulthood. This has surfaced in several other episodes since season six, leading Reese, for example, to deliberately fail his senior-year tests. Reese's boyhood has been so wasted that he is terrfied of the future, and as that future looms near his stress increases. What triggers his anxiety in this instance is the realization that Malcolm is about to leave for college. He will not only lose a brother he counts on to do the thinking for him, but also his only peer. Reese has no friends. Malcolm is his only companion. Without him, Reese's isolation will be complete. That's why he's so rankled that Malcolm is spending "the rest of the time left" not with him but with Stevie.
--Reese's lack of self-esteem. This scene is in an updated sequel to the self-loathing scene in "Experiment": "Stupid...stupid...stupid. I hate you...I hate you... ... ... And then I worked on my triceps." He is so convinced of his own worthlessness that he assumes Malcolm will never see him again after he goes off to college.
With all these anxieties lurking in Reese's mind, Stevie insults him. It's the spark that sets off the explosion of rage. Stevie is smart, he has Malcolm's respect, he has a bright future, he's going to be Malcolm's friend forever because Stevie is worth having as a friend, while Reese is about to be discarded as worthless. The combination of all these unbearable stresses pushes him to do the unthinkable; he's going to punish Stevie for being everything Reese is not and for continually rubbing it in his face with impunity.
Malcolm's response is as unsentimental and bleakly realistic as any expression of brotherly love can be: "I'm stuck with you." He makes the question of whether Reese is worthless, whether there is anything in him worth loving, irrelevant. They're brothers, that's all that matters. The same idea was expressed much more sentimentally at the end of "Grandma Sues." The boys just found out Lois was going to have another baby and they were outraged, complaining bitterly about how they couldn't possibly share their meager resources with yet another kid. Then one of them inadvertently referred to the new baby as "brother," and the scene was suddenly transformed, as if the word had a magic power. They assured Lois that they would make whatever sacrifices were needed for the new baby. This idea that the family sticks together no matter how horrible they may be to each other is a theme that underlies the whole series and is in fact the real theme of the Reese vs Stevie story.