Unfortunately, his time at Everton was not a success as the Toffees endured a terrible start to the season and Harvey was replaced by Howard Kendall as manager in early November 1990.
Everton's form improved and they climbed from 18th in early November to ninth in the final table, as well as reaching the FA Cup quarter-finals and eliminating neighbours Liverpool on the way, but Milligan failed to perform well on the pitch and made 17 appearances, scoring once, during a frustrating league campaign.
Milligan carried on where he had left off on his return to Oldham, being a key part of their midfield as they survived three seasons in the top flight and reached an FA Cup semi-final in the 1993–94 season, only being denied a Wembley final appearance when a Mark Hughes equaliser for Manchester United held them to a 1–1 draw in the first game before they were finally crushed 4–1 in the Maine Road replay.
[1] Milligan had a fine start to his career at Carrow Road, as Norwich entered the Christmas period just outside the top five and with ambitions of a UEFA Cup place.
Manager John Deehan resigned a month before relegation was confirmed, replaced on a caretaker basis by Gary Megson until the job went to Martin O'Neill after the season's end.
O'Neill left in December 1995 to take over at Leicester City, with Gary Megson returning for a second brief spell at the helm as the Canaries finished 16th after some early promise.