The show opens with the Thundercats fleeing Thundera just as it is about to explode. In the command centre are Jaga, Panthro, Tygra, Cheetara, Wilykit and Wilykat as they prepare to watch the end. Jaga sends Cheetara to bring Lion-O to watch so that he can "learn to take the bad with the good". Snarf is Lion-O's whiny nursemaid, establishing this role for the rest of the series, by complaining that he needs his sleep.
Lion-O arrives just in time to see Thundera explode and Jaga explains that it was his home. Jaga then explains that it is Lion-O's destiny to lead the ThunderCats with the help of the Nobles, who are on the ship with him.
Snarf: No mention of old Snarf I notice. Snarf, Snarf. Go ahead and take all the glory and leave it to Snarf to clean-up after you. I don't mind. Snarf, Snarf.
Jaga then takes Lion-O into the sword chamber and shows him the Sword of Omens with the embedded Eye of Thundera. Jaga tells him that it is the source of all their powers and must be protected. Lion-O is told that the Eye will awaken when needed, but that he's not yet strong enough to use the sword.
The rest of the Thundercats are called into the chamber where Jaga uses a magic cloak to clothe them and give them weapons, which is when the Mutants attack.
For his own safety, Jaga made Lion-O stay in the sword chamber against his will, commanding Snarf to protect him.
Snarf: Yep, you bet, Jaga. Snarf will keep Lion-O safe. Don't worry.
Lion-O: Aw, I don't want to be safe. Safe is boring.
The Mutants are shown to be destroying the rest of the Thunderian fleet, with the intent to board the flagship.
Once the Mutants breach the hull, they rush to find the Eye of Thundera. The Thundercats are busy fighting the boarding party while Jackalman and Slithe find the Eye embedded in the hilt of the Sword of Omens which is being held by Lion-O, but is so heavy that Lion-O can not lift it off the ground. Snarf makes an attempt to guard Lion-O, but is easily captured in Jackalman's net.
As the Mutants draw closer to Lion-O, the Eye awakens and shoots out a red beam with the black Thundercat symbol embedded in it. Frightened, all the Mutants flee back to their ship and leave. Lion-O rushes to his unconscious nursemaid as Jaga rushes in to check on them.
Panthro makes the analysis that the third planet around a sun in a distant galaxy could sustain them since they cannot make it to their intended destination after the attack.
Panthro: The best we can do is this. Not much as galaxies go.
Wilykat: It's dinky is what it is.
Panthro: See this puny little sun? I've run a galatic scan for athomspheric compatibility and this blue planet, the third one out, gives me a read out of 96%.
The Thundercats determined that the only way to survive the long trip would be in the suspension capsules which would slow down their aging considerably. But because of the damaged condition of their ship, Jaga decided he alone would stay awake to pilot the ship for as long as he could. The other Thundercats debated him on this, but being the oldest and wisest, it was his decision to make and he ordered them into the capsules. Reluctantly they agreed and Lion-O embraced his mentor in tears to say good-bye.
Jaga passes away, much like Yoda, when they are nearing the planet and puts the ship on robot pilot (autopilot). Due to a failed thruster, the robot pilot cannot land the ship as it crashes into the planet.
Snarf, the only one whose capsule opens, awakens from his capsule and finds Lion-O. Lion-O, on being awoken, is shocked to find out he has grown up, but suffers from partial memory loss. When the Mutants land and start looking for the Eye again, Snarf stumbles over the sword and brings it to Lion-O. However, Lion-O dismisses the small sword thinking it is a toy from Snarf.
Lion-O jumps into the middle of a mob of Mutants and starts to fight. Snarf throws the sword to Lion-O and the sword reminds Lion-O of what it is by an electric shock knowledge transfer. In a long moment, Jaga appears to Lion-O and tells him what to do.
Jaga: Pay heed for it is your destiny that you hold in your hand. The Eye of Thundera, the source of the Thundercats' power.
Lion-O: Yes, I remember. Sight beyond sight ...
Using Sight-Beyond-Sight to sees the sleeping Thundercats. Lion-O then calls "Thundercats Ho!" and awakens the sleeping Thundercats. They bust out of their capsules and attack the Mutants. The Mutants, although they have the advantage of numbers, flee in the face of the six Thundercats.
Panthro: Now we'll have to go about seeing if we can survive in this place.
Lion-O: We will survive and create a mighty new empire. I, Lion-O, Lord of the Thundercats proclaim it. (Holds up sword as the Eye of Thundera opens, then looks around at the others) Uh, with your help, of course.
Snarf: Well, maybe it will turn out alright and maybe it won't. Snarf