Shelbourne's woes were deepened on 25 January 2007 when owner and general manager, Ollie Byrne, was taken to hospital with a reported brain tumour, most likely, stress-induced.
The fiasco only served to increase the pressures on the FAI, who already had to find two new replacement clubs to participate in the league following the extinction of Dublin City F.C.
However, the FAI did not specifically announce whether their decision was punishment for continuing off-the-field abuses from 2006, such as failing to pay players their wages, or whether it was a repercussion of Shelbourne failing to meet the requisite criteria for partaking in the 2007 Premier Division (although it is likely that the course of action taken was due to the latter as if it were a punishment for the 2006 season a deduction in points from that season's tally would be the usual penalty, which would have led to the club being stripped of their title in this scenario).
Waterford United accepted the invitation, while the task of sourcing funds, a manager and squad before the transfer-deadline of 28 February remained at the forefront of the club's worries by mid-February.
Several of them had reached the end of their contracts, whilst some were sold shortly after the celebrations in November, and others left after being declared free agents in the courts following missed payment of wages.
Only 2 senior players remained with the club, the experienced Jim Crawford, and the young James Chambers who had spent 2006 on loan at Premier Division side Waterford United.
Shortly after this, the club's majority shareholder Ollie Byrne suffered a brain tumour and Joe Casey was installed as Chairman.
Experienced defender Alan Murphy was signed from Longford Town and was appointed vice-captain, whilst a plethora of young players arrived from a host of clubs.
Mark Leech signed on a season-long loan from Premier Division club Drogheda United, and new Derry City arrival Kyle Moran did the same.
Four players arrived at Shelbourne from Dublin rivals Bohemians; Conor Rafferty and 2006's top scorer for the First Division Davitt Walsh signed on loan deals until the end of July, defenders Aidan Collins and Niall O'Reilly made their moves to Tolka Park permanent.
Shelbourne's 2007 season in the First Division began brightly with a dogged display against Kildare County at Tolka Park less than 2 weeks after their squad was assembled.
Darren McKenna's dramatic late equaliser in that game secured a point for Shels giving the Tolka Park side much optimism for the season ahead.
With injuries to notable players such as Jim Crawford and Aidan Collins, Shels' strength in depth would face a stern test during this period.
Despite encouraging displays against Cobh Ramblers (2-2 draw) and another late defeat this time to Limerick 37 (3-2) would not be not enough to prevent numerous changes during the upcoming July transfer window.
Shels hopes of securing 3rd place were dashed over one weekend at Tolka Park with a 1-1 draw against Monaghan United and a defeat by Finn Harps with yet another last minute goal conceded.
Despite a comfortable 4-1 win away to Athlone Town, Shels struggled during this period with a defeat to Dundalk and a disappointing home draw to lowly Kilkenny City.