Bohr left Copenhagen to seek J. J. Thomson at Cambridge. While studying cathode rays, Thomson postulated the existence of what he called "corpuscles," later to be renamed "electrons" by H. A. Lorentz. This 1897 discovery ignited research worldwide, including Bohr's own, and soon the traditional picture of the atom as a solid ball was replaced by a picture that focused on the dynamic between electrons and their positively charged counterparts, protons. There was no doubt in Bohr's mind that his path lay with Thomson at Cambridge, where he headed the illustrious Cavendish laboratory.

He hurried to Cambridge as soon as was feasible and arranged a meeting. Thomson was cordial and showed some interest in the young man's work. Language barriers made their communication difficult, and Bohr tried to capture the revered man's attention by immediately pointing to some errors he'd found in Thomson's work. While this may or may not have changed Thomson's attitude, Bohr later recalled and joked about his naiveté. Bohr presented Thomson with his dissertation, and Thomson gave him some preliminary guidance on experiments to be carried out. Not long after, Bohr saw that his work was not showing much promise, and he found out that Thomson had still not read his paper.

While working with Thompson, Bohr had the chance to hear Ernest Rutherford speak. Rutherford had recently become famous with his 1911 discovery of the atom's nucleus. For years, Rutherford had been shooting alpha particles at different targets, in order to study atoms. Most of the alpha particles went through, but miraculously, every once in a while a particle would be deflected back. This discovery sent Rutherford into a long period of consideration, but he emerged with revolutionary insight. He proposed that the atom looked like a miniature solar system, with a massive center around which electrons orbited. The majority of alpha particles passed through the gold foil because of the vast space between the electrons and the nucleus, but those that were deflected back must have struck the small but mass-possessing nucleus.

Captivated by his brilliance and drawn to his personality, Bohr soon decided to move to Manchester, and Rutherford accepted him as a student. Although Rutherford was fundamentally an experimental physicist and Bohr a theoretician, both developed great mutual respect. When asked why he was able to make an exception for Bohr from his general attitude toward theoreticians, Rutherford is said to have responded, "Bohr's different. He's a football player!" Rutherford's aversion to theorizing, however, may have held Bohr back. Based on experimental evidence that arose in Rutherford's lab, Bohr began toying with the idea of isotopes (an atom of an element with the same atomic number but a differing atomic mass) and radioactive displacement (the transformation of an element to another element due to changes in atomic number). Rutherford was not convinced and discouraged Bohr from advancing theories without the appropriate evidence. Not long after, several scientists independently began uncovering the evidence that would have proved Bohr right, but Bohr never complained that he had not received any credit, nor did he blame Rutherford for discouraging him.

Instead, he continued to push ahead with advances on Rutherford's model of the atom. The fundamental difficulty he encountered was that Rutherford's model proved unstable by classical standards. According to Newtonian mechanics, the orbiting electron should lose energy as it gave off radiation and eventually collapse into the nucleus. Such a picture of course contradicted the stable physical reality of the observable world. Earlier in the century, scientists like Planck and Einstein had already begun to show the limitations of classical physics in its picture of radiation and light. Through extensive calculations they proved that thermal radiation and light are not continuous. Instead, they are made up of individual packets of energy, which they named "quanta." This radical picture of matter unsettled the scientific community and was accepted only gradually, but Bohr saw its relevance to the atomic world, which seemed to require a new set of rules as well.

He became convinced that he could determine these rules using the quantum of action (Planck's constant). He began toiling over his calculations in the spring of 1912, working day and night and determined to have a paper ready before his wedding date of August 1. Drawing on the concept of quanta, Bohr attempted to show that the atom could exist only in discrete states, each with its own energy value. This theory later enabled him to account for the series of lines in the spectrum of light emitted by the hydrogen atom. In examining this hypothesis, Bohr not only advanced the revolutionary quantum theory, but began to surmise answers to age-old questions. Most notably, his theory had implications for the nature of matter itself, and what gives the elements their distinctive properties. This work was presented to the public in the form of three articles, later referred to as the Trilogy, in the Philosophical Magazine.

He left Manchester with these fresh insights, having spent only four months there. He returned to Copenhagen for his wedding, and after a honeymoon in Norway, England, and Scotland, he was prepared to continue his work at the University of Copenhagen.