After the Master killed all the Logopolitans, an entropy wave travelled across the universe. Since the mathematicians were no longer around to divert entropic energy to the various Charged Vacuum Emboitments, which would have otherwise prevented an entropy wave from forming, an entropy wave naturally resulted, causing entropy to increase at whatever points the wave touched. Many star systems — including that which was Nyssa's home — were destroyed by the wave.
Entropy constantly grew throughout the universe as time went on. Long ago, the universe passed the upper limit for the amount of entropy allowed within it without all structure falling apart. However, the Logopolitans of Logopolis found a way to use their great skill in mathematics to solve the problem. After building a replica of the Pharos Project, they used it to send out their block transfer computations to create and funnel excess entropy into CVEs, the gaps between N-Space and E-Space. However, when The Master arrived on Logopolis, he used a sonic projector to cancel out the sound of the verbally calculated mathematics done by the Logopolitans, which in turn stops the entropy from being able to be released into the CVEs, causing a build up in the universe and instability in Logopolis which killed all the Logopolitans, preventing them from being able to resume their calculations once the silence had been lifted, and therefore letting the entropy spread. This spread of entropy throughout the Universe was called an Entropy Wave. (TV:Logopolis)
The entropy wave rolled across the universe, destroying whatever was in its path, including planets like Traken. The wave was finally stopped after The Doctor and The Master fed the Logopolitans' program through the computer at the original Pharos Project, sending the information back into space and reopening the CVEs like it did on the replica on Logopolis. (TV:Logopolis)