This has been answered in the official FAQ.
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1.14 The End Phase
Q. In what order are things carried out in the end phase ?
A. Any special events which take place during the end phase, such as critical hits on a War Engine or an Eldar Avatar leaving the battlefield, are resolved before formations rally unless otherwise specified. If both players have effects for the beginning of the end phase, take turns resolving them, alternating between players for each subsequent effect until all effects are resolved. The player with the higher strategy rating has the option of actin first or forcing the opponent to act first.
And
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Q. When exactly in the end phase does the additional damage from Plasma Reactor Hits or Gargant fires happen ?
Is it before or after rallying or repairing shields ?
A. Unless noted otherwise, things like this should happen at the start of the end phase, before you do anything else.