Previously, in May 1842, trouble had started brewing, this revolving around the additional two-tracks laid shortly after the arrival of the L&BR. The L&GR took the bold move of increasing the tolls it charged to the three other concerns using its metals, the company increasing these by just over ½ a penny per passenger. Naturally, this did not please any of the companies affected, and despite the level of disapproval voiced by the trio, their cries fell on death ears - the L&GR would not budge. As a result of this price surge, the L&CR was forced to stop running any trains and instead had the L&BR and SER carry its local traffic, whilst also competing with the L&GR’s services by means of operating a bus service between New Cross and the West End. Meanwhile, the SER and L&CR had begun planning an alternate route to London, which would avoid the L&GR lines and thus allow them to evade the high toll charges of 4½d (£1.00 by today’s prices) per passenger. On 4th July 1843, the SER and L&CR received Royal Assent for the construction of a diversionary spur to what became ‘’Bricklayers Arms’’, where a joint terminus station was to be established. Reached by a long wooden viaduct, the two concerns opened the new joint station on 1st May 1844, the SER paying for two thirds of its cost and the L&CR bearing the remainder. Named after the local pub, it was much more inconvenient for passengers who wanted to reach the City or West End, compared to its London Bridge counterpart. However, the terminus was designed as a temporary measure to starve the L&GR of the rents which, being a small pioneering concern from the outset, it relied upon for its existence. ‘‘Temporary’’ in one sense of the word, the station did incorporate a number of permanent-looking features, the most prominent being the brick-built façade, lined with stone blocks. This comprised seven arches, each 22 feet high, augmented by a centrally located clock face. The SER seemed to have an affinity for weak and poorly designed trainshed roofs, the original curved example at Charing Cross being the most renowned for collapsing. History certainly repeated itself on that occasion – the SER had experienced similar at Bricklayers Arms. A basic trainshed comprising three pitched-roof spans covered a total of six tracks and four platform faces. Twice within six years, the trainshed collapsed, the first occasion of which was unprovoked, the second time owing to a train crashing into one of the columns. However, if the SER had intended Bricklayers Arms to be a long-term solution, then no doubt a more solidly designed structure would have prevailed.
Inconvenient for passengers, Bricklayers Arms certainly had its advantages. From the outset, it became an important hub for both the SER’s and L&CR’s freight traffic, which allowed the two companies to dispense with the original goods facilities of the latter, positioned on the northern side of London Bridge station. 10½ hectares were available for terminal facilities, a yard, and for the creation of a motive power depot. Indeed, in 1846, the site also stimulated the possibility of forging an independent route to the LSWR’s proposed Waterloo terminus, but these plans were subsequently thwarted by Parliament (although the LSWR received approval for undertaking more or less the reverse of this scheme!). Nevertheless, Bricklayers Arms had served its purpose: the L&GR had been rattled.
The L&GR embarked on financial dire straits as a result of the avoidance of London Bridge by the SER and L&CR. In utter desperation, the company offered the SER a hundred year lease on its line in 1844. The SER was initially laid back, preferring to observe what else transpired first, before bailing the L&GR out of its money crisis; the former had been running a successful London to Dover via Redhill service since 7th February 1844. To alleviate its problems and coax custom back, the L&GR agreed to reduce the tolls it charged for using the London Bridge approaches. In response to this, the L&CR could again begin running into the capital’s first terminus, and in a bid to improve its suburban services, a quite innovative concept came to light. In October 1844, the company embarked on the construction of an atmospheric railway between Croydon and Forest Hill, which utilised a 15-inch cast-iron pipe laid central to the rails, fed by air pumping houses every three miles. The first test on 22nd August 1845 was successful, with a very impressive 60 MPH being reached by a formation of carriages. This initial trial was bettered in September, with the amazing speed of 70 MPH being attained. The atmospheric railway opened to fare-paying passengers on 19th January 1846, and in June of the same year, was further extended to New Cross. For all its advantages, such as increased speed, the ability of trains to climb relatively steep gradients, and the near elimination of the potential to crash, the atmospheric system had its downfall. The leather flap on the top of the pipe, which sealed the air into the system (but lifted for a passing train), fell foul to extreme weather. This was compounded by the fact that the local rat population enjoyed feasting on the material, which quickened the demise of this quite ingenious system. The L&BR absorbed the L&CR in 1846 (thus becoming the LB&SCR), and in May of the following year, cancelled the project, removing the entire atmospheric infrastructure in the process.
Meanwhile, a deal had finally been struck in August 1844: the SER would lease the L&GR’s lines for a sum of £45,000 a year (£3¼ million by today’s prices). All of the L&GR’s shareholders concurred with the terms, but the company’s founder, George Walter, did not approve. Walter thought that the L&GR was selling out too cheaply to the SER – he had previously resigned as a resident director of the L&GR in July 1837, after a financial crisis saw the shareholders effectively ‘’push’’ him out. His woes fell on death ears, and the SER’s official takeover was scheduled for midnight on New Year's Eve, 1844. This went according to plan, and by the end of 1852, Bricklayers Arms – once amusingly branded a ‘’West End Terminus’’ - had become dedicated to goods traffic and locomotive stabling.
In 1850, the SER and LB&SCR began to carve up the original London Bridge terminus site to forge separate stations, after a number of arguments between the two over usage. This year saw the demolition of the Osborne House-like ‘’Joint’’ station: the northern section of viaduct became SER territory, the southern side became that of the LB&SCR. Samuel Beazley, whom had been responsible for the design of most of the 1849-opened North Kent Line’s stations, was employed to create the SER terminus’ main station building. This backed end-on to the tracks, was three-storeys high, and demonstrated an appearance that was on a par with the northern façade of Greenwich’s main building of 1878. Of course, the latter was only two-storeys in height and incorporated a pitched, rather than flat, roof, but the similarities were certainly evident. Unfortunately for Beazley, his work was reviewed in the context of the earlier ‘’joint’’ station of 1845; his structure was not favourable when first unveiled. At least passengers waiting on the station forecourt had some protection from the elements: a canopy protruded from the top of the structure’s first storey. However, grace was at least evident on the rail-side of the building; here, the SER erected a curved overall roof, demonstrating a façade framework which was readily comparable to that which later appeared, and is still in existence at, the ex-LC&DR’s Victoria terminus. The curved trainshed provided accommodation for six tracks and four platform faces. Two were used as ‘’arrivals’’ and ‘’departures’’ respectively for the North Kent Line, whilst the remaining pair were used for main line trains to Dover. Each platform surface was separated by three tracks, the central line being utilised for carriage storage. Despite the advent of this new station, which was deemed complete in 1851, the L&CR’s original terminus of 1839 on the north side of the viaduct (which had subsequently been used by the L&GR after the station swap) remained. This still served the original Greenwich line, and comprised two platform faces separated by three tracks (the central of which was used for carriage storage). Mention should now also be made to the period of right-hand running on the original Greenwich route. The SER had opened the North Kent Line in 1849, and from 24th February of the following year, it was decided that trains from Greenwich and those from the North Kent Line would share a single ''down'' line, hence the switch to right-hand running. The original route to Greenwich received a direct connection with the SER's North Kent Line after a westward extension from Maze Hill on 1st February 1878; right-hand running was subsequently perpetuated through to Charlton Junction. At the latter, the tracks crossed over each other, which allowed trains to resume the more customary left-hand running from that point onwards. Under the SE&CR, the original London & Greenwich viaduct between North Kent West Junction and London Bridge was widened in 1901, which saw the track layout upon the arches rearranged. Consequently, right-hand running ceased on 26th May of that year, there now being eleven parallel tracks on the approaches to London Bridge.