The first major theory that tried to explain what stuff is made out of was atomic theory, which states that everything is made up from tiny little particles that can't be broken down any further and that they're separated from each other by empty space.
In 1897, J.J Thomson came up with the plum pudding model, which was based on his experiments that showed that the atoms couldn't be solid spheres and instead must have contained negatively charged particles, which we now know to be electrons.
If the positive charge in the gold atoms was generally spread out as J.J Thomson had proposed with his plum pudding model, then the alpha particles should pass right through the sheet of gold because the weak spread out positive charge wouldn't be strong enough to affect them.
Further experiments by Rutherford found that the positive charge in the nucleus is actually made up of small discrete particles which we now know as protons.
In 1913, Niels Bohr suggested a solution to Rutherford's problem, he suggested that the electrons orbited the nucleus in a similar way to how the planets orbit the sun and also that they were held in shells.
Rutherford thought that the alphaparticles would go through and some would deflect but some went through , more thank expected some deflected and some even deflected backwards.