The State of Emergency's continued bannings and repression only led to reveal the fact that the apartheid state was weak. The country had in effect become ungovernable, which coupled together with its weak economic position and international isolation, meant it could not continue as it had. It became clear to many that the only possible path forward was real reform, and more and more whites also began to call for an end to apartheid. In the light of this situation, the UDF increasingly began to work above ground, forming closer relations with Congress of South African Trade Unions (COSATU), which was only partially restricted. During 1988 the UDF acted carefully, building up its structures and organising small, discrete campaigns. In 1989 it semi-formalised its relations with COSATU, in the formation of the Mass Democratic Movement (MDM), and the two formed closer relations with the African National Congress (ANC). The MDM also began to focus more on joining together with whites, as well as allowing some contact with blacks involved in homelands. A new phase in the UDF was once again ushered in as changes were made in South Africa. By the end of 1988 a negotiated peace seemed likely, as talks took place with Nelson Mandela and with the ANC in exile.
On 24 February 1988 the UDF was restricted from performing various activities, and was in effect banned, together with 16 other organisations. COSATU was also severely restricted. Various leaders were restricted, and restrictions were extended together with the extension of the State of Emergency. The UDF was not quite sure why, in the face of negotiation, these restrictions were introduced. Nonetheless, it decided to react by continuing protest while functioning from underground. Although the change to functioning as an underground movement was not immediate, it did happen fairly easily as affiliates took over the campaigns and often people carried on as before but just under a new name. The main problems were the lack of UDF leadership and a lack of coordination between affiliates. It was in this period that COSATU began to play a leading role. At a conference, also held on 24 February, COSATU and affiliates decided that the time had come to work together with even more groups with similar political objectives. Some unions objected to these inclusions, but COSATU recognised the need for a broader struggle. It called for a 'peaceful national protest' from 6-8 June, which was in effect a call for a stayaway, although such a call was prohibited. The stayaway was supported by between 2.5 to 3 million on the first day, although numbers declined on the second and third days. The huge support showed the new unity between different organisations.
After the success of the strike, the UDF called for a broader movement and highlighted the use of such a movement. It also introduced the term 'Mass Democratic Movement' (MDM), and it said that the MDM should strengthen grassroot structures and bring in all those organisations on the periphery, thus involving them in the struggle. Many previously excluded groups, including white groups and homeland groups, were invited to an Anti-apartheid Conference organised by COSATU in September 1988. The government did not approve, and banned the conference. The idea of a MDM did not disappear, and continued to be debated through 1989 until the Conference for a Democratic Future in December 1989.
The focus for the MDM and UDF in 1988 lay in the municipal elections in October. For the first time elections for all areas, except homelands, would be held on the same day. This meant that black and white would be voting on the same day, although in different elections. The state hoped that through the elections it would get a new group of black councillors to support it, and at the same time could assess the effect the State of Emergency had had at stopping resistance. UDF strategy for the day was discussed, and although some even called for the UDF to participate in the elections, the UDF favoured boycott and said no UDF affiliate or candidate should stand in the elections, although an exception was made in white areas. The UDF was not in the position to campaign broadly for a boycott, and local groups took the initiative. In the end, the state saw the voter turnout as quite high, looking at the percentage of registered voters who actually voted, while the opposition was satisfied, as voter registration had been very low in the first place.
The effectiveness of the election campaign revitalised the UDF and MDM as it became clear that the State of Emergency had been a failure. The UDF was also strengthened by the escape from detention of both Valli Moosa and Murphy Morobe, although a setback was received in the form of severe sentences for those in the Delmas Treason Trial. During January 1989 there was an increase in hunger strikes by detainees, resulting in the release of many prisoners.
Despite steps in the right direction, it was still felt that the MDM needed to take more effective steps. By June 1989 the term MDM was being used more widely, especially to refer to the UDF and COSATU working together as a mass movement with the people and a broader following. The movement got more direction and strengthened, although confusion over what exactly the movement was continued. The Black Consciousness Leaders criticised the MDM for being an elitist movement.
In this period repression continued, although some of the worst acts during this period were as a result of Inkatha/ UDF clashes in the Natal area. These clashes, which had begun in the early days of the UDF, continued and escalated. Inkatha had not been able to join the UDF initially as a result of involvement in the homeland system. Conflict between the ANC and Inkatha had also been carried over onto the UDF, and was particularly evident in rural areas. One reason for the escalation in violence was the increasing involvement of the state of the side of Inkatha as the state had decided to work together with 'moderates'. There were attempts at peace between the groups, although the lack of organisation by the UDF after the State of Emergency made this difficult. COSATU took over after the UDF was banned, and in September COSATU and Inkatha set up a Complaints Adjudication Board. The UDF could not participate formally as it was banned, but Inkatha still criticised it for this and the Board failed. COSATU and the UDF then decided to form a Joint Working Committee to communicate peace in the region. This committee largely took over organisation and decision making in the region. Peace talks continued to fail on a regional level as an agreement could not be made with Mangosuthu Buthelezi, but did take place on local level. The conflict however continued into the 1990s.
In August 1989 the UDF and MDM organised the first major national campaign since the start of the State of Emergency. A defiance campaign, similar to that of 1952 was organised, and people took part in civil disobedience campaigns across the country. It was hoped that through the campaign mass organisation would be rebuilt, and the moral high ground won. The campaign was primarily a campaign for civil rights, and involved church leaders. Certain demands were made to the government, calling for fundamental change. The focus of the campaign differed from region to region, and ended with protests against the general elections for the Tricameral Parliament. F.W. De Klerk, the new President, called for police restraint during marches and protests, and gave permission for certain marches to take place. This showed a radical change in the government, and showed the effect of protest and of international criticism.
By the end of 1989 it was clear that negotiated change was near. The UDF participated in two conferences. The first was the Conference for a Democratic Future, organised by the MDM. The second was organised by the Kagiso Trust, and entitled 'From opposing to governing: How ready is the opposition'. The two conferences were turning points, and important in their size and diversity of participants. Their importance was however over-shadowed by the unbanning of the ANC a few months later.