Red didn't get the Silph Scope, but rather Green did and he handed it to Red. I think that Green stole it from the grunts. Also, Red never battled Marowak since she departed to the afterlife once she reunited with Cubone, so the Silph Scope was rather redundant.
Red lost to Giovanni at Silph Co. and didn't get a Master Ball, which explains why he didn't use it to catch Mewtwo. Also, it was stated that Team Rocket had the scientists experiment on Pokémon, which Red released from captivity. Nothing was said about the actual experiments, though. Giovanni only used an overleveled Rhyhorn and Rhydon in the gym battle, which were apparently his "big guns" not normally used in the gym (he used a different team against Green and lost). Giovanni's flashback established that Charmander was his starter, so I guess that Red mostly affected Giovanni by reminding him of his own past.
There was a lot of drama around Mewtwo (Green got hurt while battling it), but it turns out that Red just wanted to catch it to complete his Pokédex. That's disappointing since he even realized who Dr. Fuji was (he asked Oak to confirm his theory, but he just rambled about the stones), and yet he didn't do anything with that information. After that, he said that Mew was next on his list.
Is Origin canon? No, but I think we can infer that Red really did catch Mewtwo and Fuji's research is indeed connected to Mega Evolution. Hopefully these things will make sense in XY.
Red lost to Giovanni at Silph Co. and didn't get a Master Ball, which explains why he didn't use it to catch Mewtwo. Also, it was stated that Team Rocket had the scientists experiment on Pokémon, which Red released from captivity. Nothing was said about the actual experiments, though. Giovanni only used an overleveled Rhyhorn and Rhydon in the gym battle, which were apparently his "big guns" not normally used in the gym (he used a different team against Green and lost). Giovanni's flashback established that Charmander was his starter, so I guess that Red mostly affected Giovanni by reminding him of his own past.
There was a lot of drama around Mewtwo (Green got hurt while battling it), but it turns out that Red just wanted to catch it to complete his Pokédex. That's disappointing since he even realized who Dr. Fuji was (he asked Oak to confirm his theory, but he just rambled about the stones), and yet he didn't do anything with that information. After that, he said that Mew was next on his list.
Is Origin canon? No, but I think we can infer that Red really did catch Mewtwo and Fuji's research is indeed connected to Mega Evolution. Hopefully these things will make sense in XY.