In case you need a refresher, in the original timeline the Hargreeves were sent on a mission to find and detonate a deadly weapon inside a container, however on finding the container Ben disobeyed instruction, instead opening it and pulling Jennifer out from it. As Ben didn’t follow his adoptive father Sir Reginald Hargreeves’ orders, he shot him and Jennifer immediately.
We learn that the reason Reginald didn’t want them to interact with Jennifer is because she contains a particle element called Durango. Unintentionally created by the Reginald’s wife Abigail, when Durango interacts with the Marigold that gives the Hargreeves their powers, the two elements create a catastrophic reaction capable of destroying the entire world, AKA the Cleanse. Eek, fair enough Reg.
The Cleanse
This means that when Sparrow Academy Ben spikes his adopted siblings’ glasses with Marigold, he’s not only giving them their powers back, but also triggering a whole lot more consequences down the line.
After Ben and Jennifer meet and bond, the Cleanse begins unfolding, with the pair’s bodies morphing into one terrifying creature.
The infinite time loop
We also learn why the Hargreeves find themselves stuck in an infinite time loop, with Five discovering through a conversation with an alternate version of himself that the siblings are directly responsible for the infinite number of timelines, with the Marigold that infected the siblings’ birth mothers fracturing the original timeline into several countless alternative loops.
In order to stop the unending loop, therefore, the Hargreeves must allow the Marigold in their bodies to react with the Durango from the Cleanse and neutralise their abilities.
The final moments
Before the Hargreeves concede to engulfing themselves in the Cleanse, though, they send Allison’s daughter Claire and Diego and Lila’s three children to the underground subway station to reach the waypoint between the alternate timelines.