I've lost the muse for this and don't think I can ever really do justice to the rest of the series/changes. And because of this, I haven't written anything.

I am going to officially abandon this. For those who are interested, I will explain what I had planned:

I hadn't decided how involved the Voyager timeline would be or whether Harry would ever actually visit the Guardian of Forever. Its existence is classified and no one who heard of Harry's dreams knew of the information.

Harry with both ships in Klingon space, High Council/Gowron call for him to give evidence, changeling Martok manipulates the situation to make Harry listed as Persona non grata/Enemy in the Klingon Empire. Both ships have to cloak and warp out.

Harry returns to Deep Space 9 and the threat of attack basically causes both ships to keep their general location closer to the wormhole.

Harry travels back to Earth as a VIP guest during launch of second Griffon-class vessel, USS Thunderbird. The Changeling once again takes over the Admiral who is supposed to promote Sisko. However, Marauder's Map on Bruce uncovers the plot before the changeling can be killed by Odo, meaning Odo is not punished for killing a fellow changeling by being made Human.

Changleings do make several attempts to get Harry killed using various catspaws. Winky, recently verified as pregnant, is injured and only through intervention by Bashir her new elf child is saved.

As a result, Harry declares war and will ally himself with anyone who is against the Dominion.

Major Kira and Harry have small dalliance – not that important in the grand scheme of things. The two talk and Kyra finds out that Dax never became a love interest for Harry because of the blended consciousness thing and it reminds him too much of possession, on a visceral level. Because of Voldemort, the whole thing makes him nervous. It isn't rational but it is what it is.

The Federation/Bajoran relationship moves much as it did in canon.

The Klingons do sever their connection to the Federation because of the Martok Changeling and Gowron still is an asshole.

The Dominion doesn't start the war as obviously but the Cardassian situation does become less stable. Dukat is made irrelevant/disliked by the Cardassian government. Ironically, the changelings who influenced this make it open season on Dukat for Harry and he uses magic to finally kill the man.

A few months later Zee-al is recovered and finds her father is already dead. Kyra take her on without Dukat's slimy presence. Harry, having been behind Dukat's death, resolves to ensure she is taken care of personally but does not get into a personal relationship with her. She does end up with Garek but that's in the background.

The Dominion does make the same strategic moves as the original series. The Dominion war occurs, but to a smaller degree.

When the Dominion allies itself with the Cardassians (via a different Gul because Dukat's dead) Harry and Krim move to immediately evacuate the DMZ of Maquis/settlers. Many refuse but many send their children or those not prepared to fight to the death.

Instead of hundreds of thousands dead, tens of thousands are saved and Harry helps get them relocated to a colony further away from Cardassian space.

An extremely major change comes during the confrontation between the Prophet and Kosst Amojan. Knowing about the prophecy which said that the Reckoning had to be decided or that it would be decided later after a much more violent struggle, Harry backs Sisko's decision to not interfere and prevents Kai Winn from stopping the Reckoning.

Because it isn't stopped, the energy release of the battle causes significant damage. Both the Prophet and the Kosst Amojan finally decide it's a draw and that the Emissary must choose. The Pah-wraith tries to use his host's identity to help the Emissary to decide in his/its favor but Sisko rejects the Pah-Wraith and the Kosst Amojan is expelled.

Jake Sisko's body, however, is damaged from the battle. Harry expends every effort to heal him, calling for his elves to bring potions.

Winky's elfling, Dibby, comes with the two when Harry calls. Upon seeing Jake, who the elfling has become fond of, the small elf ties himself to Jake and uses its magic to help Harry and his parents heal him.

Jake's status as a quarter Prophet makes him somewhat magical, but not a full wizard, just as his father isn't a full wizard. But their genetics make them compatible with house elves. The House Elves are forever free but attached Bajor and the Prophets in addition to Harry and his magical descendants.

Harry is rewarded by the Prophets and led to a planet which has inhabitants who have some small magic but have no codified magical studies.

His arrival is a revelation and he has many children. He ends up being the lead educator at the new magical school. Selene Lovegwood marries into the local populace and her children do become seers.

The Elves are also made welcome and the planet will be tied to Bajor as well because of the Siskos and their descendants.

Ben Sisko does end up "ascending" to full Prophet status but a few years later and much less forced.