The Dragon Crisis was a time when Alduin emerged from the time rift he was banished to during the Dragon War. He, along with the many dragons that he resurrected, caused destruction and chaos throughout Skyrim. (The effects of this Crisis on other provinces is not directly stated, although it is clearly present beyond Skyrim.) However, the Dragonborn rose and was able to defeat him as foretold by the Elder Scrolls.
During the time of the human rebellion of the dragon rulers, three heroes, with help from the dragon Paarthurnax, were able to defeat Alduin using an Elder Scroll. They were not, however, able to completely destroy him, but rather send him in a time rift through the Elder Scrolls in the form of a Dragon Break.
Order of Battle
Sacking of Helgen
Alduin exited the time rift during the Civil War, in 4E 201. At the time that the Stormcloaks and the Imperials were fighting over possession of Skyrim; additionally, the Dovahkiin was attempting to cross the border of Cyrodiil, only to be captured in an Imperial trap along with many Stormcloaks, including their leader, Ulfric Stormcloak, and Lokir, a horse thief. After they were escorted to Helgen, where their execution sentence was to be carried out, Alduin attacked. In the confusion, the Dovahkiin escaped through Helgen Keep accompanying either Ralof (a Stormcloak soldier) or Hadvar (an Imperial soldier). The pair fled to Riverwood, where family members of both soldiers lived.
Death of Mirmulnir
After recuperating in Riverwood, the Dovahkiin carried news of the attack to the Jarl in Whiterun. After speaking with Jarl Balgruuf the Greater, the Dovahkiin was directed to Farengar Secret-Fire, who bid him retrieve the Dragonstone from Bleak Falls Barrow. Upon returning the stone to the court wizard, a guard reported a dragon attacking the Western Watchtower. Jarl Balgruuf bid the Dovahkiin go with his housecarl, Irileth, and several guards, to defeat the dragon. It is here, after defeating Mirmulnir, that the Dragonborn was proven to be the actual Last Dragonborn. When reentering Whiterun, the Dovahkiin, and essentially everyone in and around Whiterun, heard voices coming from the Throat of the World, later revealed to be those of the Greybeards, summoning the Last Dragonborn to High Hrothgar.
Training with the Greybeards
Receiving the news of being a Dragonborn and hearing the call of the Greybeards, the Dragonborn traveled to the small town of Ivarstead and proceeded to climb the Seven Thousand Steps. After entering High Hrothgar, the Dragonborn spoke to Arngeir, one of the Greybeards. Arngeir asked the Dragonborn to demonstrate their abilities on him and the other three Greybeards, and, after doing so, the Greybeards presented a test for the Dragonborn; the Dragonborn had to use their new ability on three spectral forms. After completing the test, the Greybeards and the Dragonborn proceeded to walk outside to the courtyard for another test. The Dragonborn immediately learned a new Shout, known as Whirlwind Sprint.
After demonstrating the new ability, Arngeir then spoke to the Dragonborn and informed them that their training was complete, but that a final trial was given by him and the Greybeards to retrieve the Horn of Jurgen Windcaller, located in Ustengrav. The Dragonborn went to Ustengrav and discovered that the Horn of Jurgen Windcaller was not there. A note was on the pedestal where the Horn should have been, but the note contained instructions for the Dragonborn to travel to the Sleeping Giant Inn in Riverwood; the note was signed simply by an entity calling themselves, "A friend."
After arriving at Riverwood, the Dragonborn went into the Sleeping Giant Inn and requested for the room in the attic from the innkeeper, Orgnar. He replied that there was no such room, and quietly told the Dragonborn to go to the room on the left. As the Dragonborn walked over to the nearby room, a woman walked over to the Dragonborn and speaks to them. She revealed that her name was Delphine, and that she was the one who took the Horn of Jurgen Windcaller and left the mysterious note. After a short conversation, Delphine revealed to the Dragonborn that she was a member of the ancient order of the Blades, renowned for their feats of dragonslaying, and that she also knew about several dragon burial sites located across Skyrim, one of which being at Kynesgrove, in Eastmarch. She believed that the dragons were being resurrected, and that the next resurrection would happen at Kynsegrove. She asked the Dragonborn to either travel with her or meet her at Kynesgrove, to discover what was going on with the return of the dragons.
Battle of Kynesgrove
After arriving at Kynesgrove, Delphine and the Dragonborn rushed up the hill to where the Dragon burial site was, as residents were tying to get inside their homes for safety. After getting to the top of the hill, Delphine and the Dragonborn hid behind a rock as they observed one of the most awe-inspiring, but surprising and disturbing, sights in Skyrim's history. A massive, black, scaled dragon hovered over the burial site, speaking in the ancient Dragon Language, as another dragon was rising out of the burial site. The massive, black dragon that was resurrecting the dragon revealed himself to be Alduin, the World-Eater, the Nordic God of Destruction who was the leader of all of the dragons on Tamriel during the Merethic Era when they still existed. The dragon who was being resurrected was Sahloknir. Alduin also spoke to the Dragonborn, telling them that they were an embarrassment to the race of dragons, and that their Voice shined not from Dragonkind, but from their own self.
Alduin then ordered Sahloknir to "slay the mortals," and then as Alduin flew away, Sahloknir began to attack Delphine and the Dragonborn, and a battle ensued. Eventually, the Dragonborn and Delphine were able to kill the dragon. Following Sahloknir's death, the two conversed on what happened, what to do next, and for information to be revealed. Earlier, at Riverwood, Delphine promised the Dragonborn to reveal everything about herself and what she knew, after they dealt with the Dragonborn at Kynesgrove. After Delphine revealed more information about herself and what she knew, the two discussed on what to do next. Delphine believed that the Thalmor had something to do with the return of the dragons, and if they did, the Dragonborn could use that information to stop the Dragon Crisis. Delphine had a contact in Solitude, the capital of Skyrim, Malborn. The Dragonborn had to meet Malborn in Solitude and discuss the specifics of the mission.
The Throat of the World
When returning to the Greybeards, the Dovahkiin met with their leader, the dragon Paarthurnax. Paarthurnax then sent the Dovahkiin to find an Elder Scroll.
Hunt for the Elder Scroll
The Dovahkiin traveled to the Dwemer Ruin of Blackreach, where the Elder Scroll (Dragon) was contained within the receptacle of the Oculory inside the Tower of Mzark. The Dovahkiin extracted the Elder Scroll from the Oculory and returned to the Throat of the World.
Duel atop the World
Once the Dovahkiin acquired the Elder Scroll and traveled back to the Throat of the World, they discovered how Alduin managed to come back to Skyrim. After reading the Elder Scroll, the Dovahkiin fought Alduin, with the help of Paarthurnax, and together they nearly defeated Alduin during the "Duel Atop the World" quest by using the mortal-made shout Dragonrend, the very shout used to defeat him long ago. Despite their best efforts, however, Alduin managed to escape to Sovngarde.
The Final Battle at Sovngarde
The Dovahkiin convinced the Jarl of Whiterun to allow them to use Dragonsreach as a prison for Odahviing, Alduin's second-in-command, in the hopes to learn where Alduin escaped to. After the dragon's capture, he confessed that some dragons began to doubt that Alduin was truly the strongest amongst them. He then struck a deal with the Dovahkiin, which was to free him; in exchange, he would carry the Dovahkiin atop his back to the gate of Sovngarde, located at the Nordic ruin Skuldafn. After reaching Skuldafn, the Dovahkiin defeated the Dragon Priest Nahkriin who was guarding the portal, then teleported to Sovngarde. Teaming with the three warriors who first defeated Alduin, the Dovahkiin defeated Alduin in the Battle of the Tongues.
In the aftermath of Alduin's defeat, most of the remaining dragons recognized the Dovahkiin as a superior, (or, at the very least, as an equal) to them, and agreed to cease their hostilities, acknowledging them for the power of their Thu'um and the defeat of Alduin.
However, if the Dragonborn did not kill Paarthurnax, the Dovah acknowledged them as their king, with Paarthurnax stating his intention to bring The Way of the Voice to all dragons.
Alduin's former second-in-command, Odahviing, swore loyalty to the Dragonborn, after witnessing the Dragonborn's power for a second time.
In either case, however, some dragons still acted to terrorize Nirn. This suggests that not all dragons followed their leader, and therefore making it possible there were some dragons who did not listen to Alduin.
The Dragon Crisis also had a heavy impact for Miraak's machinations in Solstheim; the man, also a Dragonborn, hoped to fulfill his own agenda of domination over Tamriel by killing the Last Dragonborn and claiming their soul in order to escape Apocrypha. But ultimately, he was defeated by his rival and slain by his master, Hermaeus Mora, as a punishment for his rebellion against him, and his soul claimed by the Dragonborn, along with the souls of many dragons claimed by Miraak.