The evidence for the existence of a nucleus in an atom comes from these observations in Rutherford's experiment:
(1) Few of the rays get deviated from their path.
(2) One out of 12000 rays return on their path
From these two observations, the following conclusions can be drawn that support the existence of a nucleus in an atom: -
(1) Deviation shows the presence of some positive particle.
(2) The returning back of the ray on its own path shows, there is something which is solid in nature and its number (i.e 1/12000th ray) shows the particle is very small in size.